A strict deterministic physicalism is very difficult to reconcile with

our sense of how thinking ought to work-- this is partially the

argument Plantinga is making above, but this difficulty of naturalism
predates him.
The easiest demonstration of what I mean is something like this: we
immediately discount thoughts that we know (or strongly suspect)
to have physical causation. We think of the "real" Phineas Gage as
the one without the railroad spike in his head. Or, for another
example, we discount many things drunk people do, because we
know it is caused by alcohol. Ditto for schizophrenics, etc.
But this is inconsistent: all thoughts in a physical system are
ultimately externally caused. Why should some thoughts be
privileged? Shouldn't I discount your thinking because I "know" it is
only the random motions of atoms in your cranium?
For that matter, how do you ever have relevant thoughts at all?
Since all of your thoughts are ultimately part of a long chain of
external causation reaching far into the past, doesn't it strike you as
remarkably odd that you can think about your spouse when you
hear their car roll into your driveway? Why should your neuronal
activity correspond to relevant subjects that aren't present?
So, in this objection, naturalism is difficult to live with consistently
because we feel-- and universally act-- as though our
thoughts are privileged. We differentiate between
thoughts caused by something external to a person vs thoughts that
somehow arise internally.
Yet naturalism, if we're consistent, doesn't seem to allow for this
distinction. (Plantinga is making a more specific sub-argument
re:specifically what we should expect, epistemologically, if
evolutionary naturalism is true.)
I'd also point at ontology as another difficulty. Human beings pretty
universally act as though identity were a real and tangible thing.
Further, we routinely recognize each other, even after decades have
passed and many changes have occurred-- including the
replacement of every atom in our body.
If you're an idealist, a dualist, or any number of other ontological
positions, you have wiggle room to define identity. Yet in a
materialistic system, identity makes no sense-- everything is flux,
and there is no rational sense in which one is the same person as
yesterday.
Yet human beings speak and at as though identity is a real thing. I
say that I love you and only you-- or I say, "That's not the person I
know and love." It's not impossible to try and explain this in
materialistic terms, but it requires a lot of complex maneuvering
where other positions do not.

Then there is the classic is/ought difficulty.

Basically, in a materialistic system, one cannot possibly use the
word "ought" rationally. One can be descriptive, but not
proscriptive.
So, if you murder me in cold blood-- for example-- in a materialistic
system we can very consistently say things like:
Society sends people who murder others to jail if they are caught.
Most human beings are shocked and horrified by murder and
believe those who murder should be punished. Murder destroys
social cohesion.
That is, we can describe the beliefs people generally hold about
murder. We can state that murder in our society carries such and
such a punishment.
But what you cannot say, rationally, is murder is wrong. Not in the
way we want to. Because the first and obvious rejoinder is: "Says
who?"
That is, without a god or some sort of pantheistic "ground of all
being", you have no higher power to create, enforce, or justify a
universal moral proscription.
Can a naturalistic ethics be created? Yes! Would it be perfectly
consistent to say that human beings evolved to have social
constructs that enable advantageous group behaviors? To say that
however we feel, whether it's a universal or not, most human
beings will act in a certain fashion we describe as moral? Yes!
But that's not what we want, and it's not how we talk about
morality, or treat it in actual fact. We want to say that pedophilic
rape is wrong for everyone, everywhere-- that it's evil, and those
who do it are evil, and it doesn't matter what their culture approves
of, or whether they think it's all right. That is, we want a universal-a standard that is above anyone's opinion, or any group's culture.
Even for mundane moral matters, we argue as if there is in fact
some kind of universal standard that everyone agrees on:
when I accuse you of stealing from me, you call me a liar, or try to
show I'm mistaken, or outline how it was a misunderstanding and
you were just borrowing, or you pin the blame on someone else.
But you don't just say: "So what? Who cares about your morality?"
No one looks at you like you've lost your mind for acting as though
there is some universal standard-- but in materialism, there isn't
one.
A related issue is punishment.
We treat insane people, but we punish criminals. That is, we act as
though criminals had some choice in the matter,as well

as considering their punishment not just to be rehabilitating, but

also deserved.
In a deterministic and materialistic system: why? The criminal was
predetermined by a cascade of external causes. Their crime was as
inevitable as the rising sun. They're as little capable of diverting
course as a mental patient.
Moreover, there is no sense in which they can "deserve" a
punishment. (No doubt you're sharp enough to notice that this is a
subset of the is/ought problem: "they deserve" is another way of
saying "they ought".)
So if we were consistent, we'd never talk about or treat criminals as
morally culpable-- there's no room for evil, onlysick. (And even that
is flaky: how is one state "preferable" to another? There is no
normative ideal-- why should we call this person "sick", and that
person "well"?)
Last, but not least-- naturalism has more difficulties with
consistency, but I'm long winded enough and hitting the high
points-- is the problem of qualia.
Qualia is a problem for everyone, but it's most acute for naturalism,
imo. (An excellent and accessible summation of the qualia problem
can be found in Thomas Nagel's What is it Like to be a Bat?.)
At its most basic, the problem of qualia is this: subjective
experience seems to be separate from, or an addition to, objective
and physical things.
The color red can be objectively defined as a wavelength of light of
so many fractions of a meter. Indeed, except in exceptional
situations such as color blindness, this wavelength of light
will always correlate with our perception of the color red.
Yet it seems to us that-- and we certainly act as though-- our
perception of the color red, our experience of it, is something very
different from, and not reducible to, some more objective
description such as, "Light of such and such wavelength striking
photosensitive cells properly ennervated by an anatomically and
cellularly normal brain", etc.
Those subjective experiences, we'd collectively call "qualia". Pain is
also a good example. While it may be true that one cannot
experience pain without certain kinds of nerve cell activity,
it doesn't seem to be true that the nerves firing are the "whole
story", so to speak. Mere nerves firing does not explain whatever it
is we feel when we feel pain.
But in a materialistic universe, this is a bit baffling. You can't hold
an experience of pain, you can't count it or put it on a scale and
weigh it. While it seems to require certain parameters of mass and

energy to occur, the experience itself isn't made of mass and

energy, and when it occurs, the associated mass and energy may be
similar but is in no way unique (that is, there is no completely
unique and 1 for 1 causative relationship).
Moreover, we not only act as though this has an independent
existence, we can talk intelligent about, agree on, and share with
each other, to some extent, this experience.
That is, it appears to have some external existence outside of any
given creature, but no easily quantifiable objectivedescription in
terms of physical quantities.
How can something in a materialistic universe appear to be an
emergent or supravenient thing, having an independent existence,
yet not being reducible or exhaustively explained in physical terms?
So, those are a few major difficulties with naturalism. Philosophy of
math, and the unreasonable effectiveness and predictive power of
math-- what mathematics actually are, and why it works-- are also
thorny in a materialistic world. For example, physics is rife with
examples of some abstract mathematical object or formula,
uncovered and explicated without any reference to the real world,
that is forgotten for decades or centuries before it's discovered that
it actually perfectly models a very real process in the actual world.
What are the odds that some subjective machination, entirely
abstract and subjective, should later match perfectly with
something physically real?
Anyhow, this is way too long already and no one will read it (nor
would I blame them). I leave off on this note:
Let me be clear that I am only outlining problems that are difficult
to consistently believe and/or act on as a naturalist.
The distinction is that a lot of these aren't an issue of whether
naturalistic determinism is true, in the sense of being the actual fact
of the matter.
For example, while it may be irrational for you to believe that your
personal belief in naturalism likely to actually correspond to the
world-as-it-is (as opposed to being the entirely unrelated byproduct
of externally caused atomic motions in your brain)-- that isn't an
argument that naturalism is untrue.
Indeed, it could certainly be the case that naturalism is true, and
your belief in naturalism is just a coincidence.
That is, you can't rationally believe that naturalism is true-- that
believe is without warrant-- but naturalism can be true whether
you're "allowed" to believe it or not.

Similarly, while I would find it very odd for human beings to

universally believe and act as though they libertarian free will when
they are in fact determined-- that is an epistemological objection,
not an ontological one. There is no contradiction in human beings
believing one thing and the opposite being the case.
So, while there are more fundamental philosophical objections to
naturalism, I want to make clear that I'm responding to the
question: "What do you mean by [naturalism] being difficult to act
consistently with?"
The fact that we ask someone to pass the salt shaker, send
criminals to jail, argue as though there were some universal moral
standard, think pain exists as its own thing, or talk about our
identity as though it were something real-- that's a description of
what people fairly universally think and do. And none of it means
that naturalism is untrue.
But, if naturalism is true, those are all actions and beliefs that carry
the a priori assumption that naturalism is not, in fact, true.
If we were consistent naturalists, we'd never choose to ask
someone to pass the salt shaker (surely the chain of events leading
to this moment have predetermined whether they will or won't-and are more sufficient or efficient causation than our vocal chords
vibrating), punish criminals (it's not their fault, never mind it's
irrational to say they ought to not commit comes), trust our own
thoughts (they're as physically determined or random as a
lunatic's), or talk about being in love or seeing red (more proper to
describe the pattern of nerve impulses)-- among other things.
So I've no quarrel with naturalism being true-- but if you say so, I'll
be highly suspicious. You lunatic.