http://stackoverflow.com/questions/318398/why-does-c-compilation-take-so-longIn C#, List<T> is the only type that is compiled, no matter how many instantiations of List you have in your program. In C++, vector<int> is a completely separate type from vector<float>, and each one will have to be compiled separately.
Add to this that templates make up a full turing-complete "sub-language" that the compiler has to interpret, and this can become ridiculously complicated. Even relatively simple template metaprogramming code can define recursive templates that create dozens and dozens of template instantiations. Templates may also result in extremely complex types, with ridiculously long names, adding a lot of extra work to the linker. (It has to compare a lot of symbol names, and if these names can grow into many thousand characters, that can become fairly expensive).
And of course, they exacerbate the problems with header files, because templates generally have to be defined in headers, which means far more code has to be parsed and compiled for every compilation unit. In plain C code, a header typically only contains forward declarations, but very little actual code. In C++, it is not uncommon for almost all the code to reside in header files.