CMake's wildly, wildly non-obvious, and I mean that relative to autotools. ./configure && make all install is a very well-understood concept. The CMake equivalent seems to be '????? bees aojksdf'. Building projects using CMake without very detailed and specific instructions is a nightmare, and when you turn to the documentation it's several thousands of treatise on the theory of configuration and build management. Kind of like how Arch/TLA help was simultaneously very enlightening and totally useless.
CMake is a pain to use for developers. install target? Who needs it? Sort it out yourself. And the lack of standardised and first-class pkg-config support is totally unforgiveable. It's 2013 and you're making people roll their own. Not even close to good enough.
The most frustrating thing about CMake is that it was designed to replace and improve upon autotools. God knows there's plenty of room in that space, but CMake is worse for users, developers, and distributors.
(And yes, 'oh but you should just switch your project to some non-standard tool very few people understand or have installed' is really infuriating advice to be given.)