There's more to computing than user-level applications. "Compatibility" here means that you can accomplish the same tasks using different software written to attain the same ends. Since there are many users, it's profitable to port the software to multiple platforms.

When a programmer talks about compatibility, he means the operating system API. It's nontrivial to port software that uses the Windows API to anything else. This goes for pretty much any other OS architecture; porting OpenVMS software to Windows is also fraught with peril. If you have custom software, the cost to port to a new platform is enormous. Hundreds of thousands of dollars for a single server application. Millions, in many cases.