Keep in mind that at the time Microsoft was being sued for being anti-competitive behaviour by Netscape and there were a lot of attention on the company for being a bad actor. Most of Microsofts's patents were defensive (they rarely used them offensively to my knowledge). There was a group of execs that were nervous about Linux but the lack of UI/UX/Usability strength put most of the focus on server capabilities. To this day many people want Linux to be a broader desktop OS but the only strong and focused effort on this are ironically ChromeOS and Android.