The answer is: it depends.
I'm currently using MSVC compiler and GCC for a project at work and my experience is that they both do a pretty good job. Furthermore, the cost of a function call in native code can be pretty small, especially in functions that do not need to be accessible outside the executable (like functions not exported in a shared library). For these functions, there is more flexibility with how the call is actually implemented.
A few things to note: it's much easier for a compiler to optimize calls to static functions. Functions with external linkage often require link time optimization since one must know how and where the function is actually called, as well as the implementation, to do much optimization or inlining. This requires examining more than one compilation unit at a time.
I would say that you should use functions where it makes sense and makes the code easier to read and maintain. In general, it is safe to assume that the cost is smaller than it would be in JavaScript. But in the end, you'd have to profile the code to say anything more precise.
UPDATE: I want to emphasize that functions can be inlined across compilation units, but this requires link-time optimization (or whole program optimization). This is supported in both GCC (https://gcc.gnu.org/wiki/LinkTimeOptimization) and MSVC (http://msdn.microsoft.com/en-us/library/0zza0de8.aspx).
These days, if you can beat the compiler by copying the body of a function and pasting it everywhere you call that function, you probably need a different compiler.