One reason why proof by contradiction is difficult for students is because mathematical notation (and other written language) does not allow for a subjunctive mood.
Let me elaborate on this: In English and other "natural" languages, we can distinguish between a state of affairs that is true, and a state of affairs that can be provisionally thought of as true. We can say:
I am the President of the United States, and therefore I support this legislation
but we can also say
If I were the President of the United States, then I would support this legislation
and we understand these two sentences as meaning very different things. Mathematical notation, however, elides or erases those shades of meaning: If $P$ is the proposition "I am the President of the United States" and $Q$ is the proposition "I support this legislation" then both of the two sentences above
would be symbolized as $P \implies Q$ or written as "If $P$ then $Q$".
What does this have to do with proof by contradiction? Consider how one starts a proof that $x^2=2$ has no rational solutions. We say:
Suppose $x = m/n$ is a solution, with $m, n$ relatively prime whole numbers. Then $m^2 = 2n^2$, so $m^2$ is even, which means that $m$ is even. Therefore...
Now, in the above proof, consider how you would read aloud the equation $m^2 = 2n^2$. I strongly suspect that most people would read it as
"$m$ squared equals two $n$ squared"
rather than as
"$m$ squared would equal two $n$ squared"
This is precisely the sticking point: We read the symbol $=$ as saying (falsely!) that two things are equal, rather than as saying (correctly!) that two things would be equal if the initial hypotheses were true. The absence of a subjunctive mood in mathematics leads us to say things like
"Suppose $m/n$ is a solution; therefore..."
when what we really mean is
"Suppose $m/n$ were a solution; then..."
This observation, by the way, has been made before: A few years ago I came across a very brief article from The Mathematics Teacher, published more than 60 years ago, that made essentially the same argument. The article is
Butler, C. (1955). "A note on the statements of theorems and assumptions." Mathematics Teacher, 48, 106-107.
The Butler article does not explicitly invoke the subjunctive mood by name, but expresses the same idea, as the following excerpt shows (all emphases in the original):
Such apparent discrepancies... do bother immature high school students who are just learning what a demonstration means. To them it doesn't make sense to say "assume that $\angle x = \angle y$" when they can see from the diagram that angle $x$ actually is not equal to angle $y$, or to conclude that $RS \hskip{0.05 in} || \hskip{0.05 in} PQ$ when those lines can be seen actually to intersect in the diagram.
On the other hand, most students, even though mathematically immature, would find no difficulty in accepting the statement that "IF angle $x$ WERE equal to angle $y$, then $RS$ WOULD BE parallel to $PQ$" as a reasonable statement even though the diagram does not appear to exhibit these conditions.
To cite a non-geometrical proposition which is the exact counterpart of the foregoing example, it might easily appear ridiculous to young students for a $5 \frac{1}{2}$ foot man to say "Assume that I am $9$ feet tall; therefore I can touch the ceiling," but the same students would readily accept from the same man the statement, "IF I WERE 9 feet tall, THEN I COULD touch the ceiling" and regard it as a perfectly normal kind of statement.
Logically there is no difference between saying "Assume this is true; therefore that is true" and "If this were true, then that would be true," but there is a profound difference in the attitude or feeling induced in immature students by the two forms of statement.
Notice in particular that Butler realizes that a symbolic expression like "$\angle x = \angle y$" would be read as "angle $x$ is equal to angle $y$"; the only way to invoke the subjunctive mood is to drop the symbolic language altogether and use verbal formulations instead.