It's reputational protection--the same reason whistleblowers in the real world prefer to be anonymous.  If you think about it and try to put yourself in the shoes of someone who might not have a very strong personality, one that can withstand criticism from lord knows how many members on a discussion forum, it's not that hard to understand why.

Personally I don't have a problem with people using alt accounts that way, and if I ever said otherwise I'm retracting those statements here and now (lol).  What happens when you've got a real problem with a member with whom a mutual friendship/trust/respect has developed?  There are some members who'd rather deal with it via an alt account rather than confronting that person directly.  Yeah it sounds weak, but there's nothing shady about it as long as the argument being made is sound.