Makefiles work fine in the trivial case, the problem is that things quickly become complex. Automating that complexity seems like it should be easy but, as it turns out, it isn't.
There should be a way to $FOO. Well, there's a way to do it in a Makefile but figuring that out is harder than should be, and doesn't make sense when you finally do figure it out.
"Well that way is stupid. Here's how I'd do it:"
I like cmake, and used to use it exclusively, but after running into so many issues with their homebrew scripting/configuration language, I've mostly moved on. I wouldn't be surprised if I end up coming back, and I'd encourage everybody to give it a shot (the ease of typical simple Makefile generation, but with extra muscle), but the omission of Tcl as a control/config tool has always baffled me.
[0] http://en.wikipedia.org/wiki/CMake#History
[1] http://en.wikipedia.org/wiki/Insight_Segmentation_and_Registration_Toolkit
edit: formatting