The big difference is Lean and Mean network speed vs. MS Bloat on windows. That being said you get what you pay for. Linux requires a lot of care and feeding for initial setup and work for every alt coin out there require a recompile of code. Windows the executables are available to download no mess no fuss.

Linux is not for everyone. If you are a software engineer linux is a given for mining rigs. For the avearge Joe windows is easier for the masses. performance is a wash that are about the same. Windows has better drivers and over clocking utils. Linux has lower network latency and will run for days/weeks without locking up.