Linux doesn't "just work" on Apple hardware. None of the major distros can currently get the Ethernet adapter on recent Mac Minis working. As a result, we have to run OS X on a bunch of Mac Mini servers we've planned to run Linux on.
Just curious, if you were just planning on running Linux, why buy Mac Minis?
For the hardware, I'd assume?
In the past few years we had a lot of success using Mac Minis with OS X as servers. With the latest batch of Mac Minis we have purchased we tried to move over from OS X to Linux, partially because people tend to be more familiar with administering Linux servers and partially because OS X as a server can be a bit quirky.