The fragmentation, the inconsistency, the need to drop into a terminal to debug certain things, and the difficulty of dealing with driver problems for inexperienced users all do more damage than anything Microsoft attempted to do.
GUI program not running on Linux? Find the CLI call, run in terminal, grep and analyze the logs, find the error.
GUI program not running on Windows? Eh, good luck digging through the eventlog and 90% see nothing.
Have you used Windows recently? At least the former is a growing problem. Dropping down into the registry to change or create keys is no cakewalk either. If you're an inexperienced user, you're in trouble on Linux and Windows both.