A native speaker corrected a learner's sentence from

> やっぱり紅茶はコーヒーより美味しいと思う

to

> やっぱり紅茶がコーヒーより美味しいと思う

I think 紅茶はコーヒーより美味しい sounds perfectly natural.

Using は with 思う also seems to be commonplace which I have always taken for
granted. Come to think of is though, it is interesting how 物理は難しいと思う is
natural with は although things preceding と思う could be bracketed as a content
clause (dependent clause). So I wonder if the reason for that correction could
be that dependent clauses call for が? But if that's the case why do a lot of
と思う sentences use は?
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particles particle-は particle-が は-and-が
紅茶がコーヒーより美味しいと思う
This が is an exhaustive-listing-ga, and whether it's desirable depends on the
previous context. You know when to say 私 **が** 英語ができる instead of 私 **は**
英語ができる, right? The と思う at the end of the sentence does not affect this
particle choice.

やっぱり紅茶がコーヒーより美味しい should be used when the speaker is faced with a choice
between the two options (tea vs coffee). For example, if this statement is
uttered after "Many people like coffee after lunch, but I don't like it", then
が sounds more natural (は is not incorrect, though).
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As naruto's answer suggests, that it is a と思う sentence does not matter here.
And if I were correcting, I would say やっぱり紅茶はコーヒーより美味しいと思う is just fine (as a
standalone example).

You can understand the difference by standard difference for は/が. は is a topic
marker, so 紅茶は... is a simple statement about 紅茶 while 紅茶が... is 排他 (this
should be the same as exhaustive listing), implying 'tea and not something
else'.

* * *

One thing that comes to my mind is the difference may be kind of similar to
indefinite/definite article in English.

  * 物理は難しい Physics is a difficult subject.
  * 物理が難しい Physics is the difficult subject (of the subjects discussed in the context).

Similarly 紅茶は.. is like 'Tea is a better stuff' and 紅茶が... is like 'Tea is
**the** better stuff'. Logically speaking, the latter is more correct if the
sentence talks about just tea and coffee.
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In addition to the other answers (which have good points) I think another
factor to consider is what the focus of the sentence is supposed to be.

Using は establishes that thing as the topic (central focus) of the sentence,
so saying 「紅茶はコーヒーより美味しい」is specifically _making a point about (black) tea_ :
"Regarding tea, it is tastier than coffee"

However, using が does the opposite, it puts the focus on
the「(コーヒーより)美味しい」part, and just says that _tea is the thing which satisfies
that condition_ (i.e. "tea" is the answer to a (possibly unspoken) question):
"In terms of tastiness, tea is better than coffee."

I actually also don't entirely agree that the と思う part is completely
irrelevant. It's true that is not a major factor, and the other points that
have been made apply the same whether it is there or not, but when it is
present there is also a slight nuance that applies to と思う as well, depending
on whether は or が is used. This is because the topic (は) always applies to the
whole sentence, while the subject (が) usually only applies to a particular
sub-clause, so if you say 紅茶は that actually makes it the topic of not just
美味しい, but also the verb 思う too. What this means is that if you say:

> 紅茶はコーヒーより美味しいと思う

That will be parsed as:

> 紅茶は((コーヒーより美味しい)と思う)

so you are basically saying:

> I am thinking about black tea, and what I think about it is that it is
> tastier than coffee.

But if you use 紅茶が then that usually would only apply to the local sub-clause,
so:

> 紅茶がコーヒーより美味しいと思う

would be parsed as:

> (紅茶がコーヒーより美味しい)と思う

which says basically:

> I am thinking in general, and I think that tea is tastier than coffee.

Of course, none of these are inherently wrong things to say per se, but which
one actually makes sense or feels natural will depend a lot on the particular
situation, for obvious reasons.
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