Through the various areas of mathematics I’ve studied, one always stands out as the most challenging for the majority of students: Galois Theory. Of those that make it far enough in algebra to reach this level, many of them struggle with it. Rightfully so, too. It’s damn hard.
I’d say algebra is probably the toughest in its own right: lots and lots and lots of definitions and many students dislike that. Things like analysis, linear algebra, topology: they’re a bit more intuitive, at least to me and several students I know.