It's difficult to accept non-latin characters in usernames without making username spoofing trivial. For example, I could sign up for an account as `аw3c2', pretending to be you. What looks like `a' there is actually `а', a Cyrillic letter with its own Unicode code point. Assuming a website where user impersonation is an issue (say, an auction site where a homoglyph attack could be used to scam a seller into sending the goods to a different address), one would need to blacklist all likely homoglyphs and duplicate characters, or just stick to ASCII. (I'm sure users are accustomed to using ASCII usernames, though it's not ideal.)
It also makes it hard for users to log in using a dumber input device than usual.
Then there is unicode normalization. OSX might decide to encode "e-with-an-accent" as two code points, while Windows will combine them into a single code point. Users will not be impressed if they can't log in because their OS doesn't use the right encoding and the web site forgot to normalize.
