He's totally missing the point of studying computer science. It doesn't matter if you are using Linux or Windows during your studies; a proper education in CS

He's totally missing the point of studying computer science. It doesn't matter if you are using Linux or Windows during your studies; a proper education in CS will give you a foundation on which you can easily adapt to any platform, language, or environment. My school was almost entirely Unix-based, and my first job was with Microsoft. They weren't concerned at all about whether I was familiar with the Win32 API, C#, COM or anything similar - and this attitude was consistent across all new hires, not just college hires. Most competent companies (the ones you want to work for) will recognize this as well. But in any case, there are an enormous number of jobs that do not require knowledge of Microsoft-based technology.