The single biggest issue is the community's bad habit of hand-waving away these issues when they're brought up. I could (and have in the past) make a long list of all the problems that plague me as a Linux desktop user, but there is a default dismissal answer to each and every one of them as to why I'm just being a big baby and it's not actually an issue. My gut tells me Microsoft is somehow behind this.
Jokes aside, free desktop needs to grow up before it can expect to be embraced with market share. Until then, people are going to keep using Windows, and people are going to keep wondering why, while dismissing Windows users' answers.