Perhaps, but not any that I have had problems with.

E.g. an application that we distribute uses Qt, Boost, Berkeley DB XML, libxml2, libxslt, etc. Producing signed application bundles for OS X, MSI installers for Windows, and packages for Ubuntu has been nearly painless. And that's with clang on OS X, Visual C++ on Windows, and gcc on Linux. If it's easy to produce binaries on the three most popular platforms, with three different compilers, I don't see the problem.

We have tried autotools before. But it's a pain on Windows with Visual Studio. Let alone that I can quickly generate a Visual Studio project to do some debugging.