I've personally never had a problem using Cryptsy.. apart from their API. That sucks.
Otherwise.. they are reliable. Their trading engine just works. Deposits and withdrawals can occasionally have delays but it's to be expected with the vast number of sh*tcoin wallets that they try to accommodate.
As to the original question, I'm not sure why they get so much hate. I think early on the site was incredibly slow, and this probably contributed.
It's probably more down to this though..
They were the biggest exchange for a long time, and every new coin they added was pumped almost instantly, then dumped just as quickly, and this is what mostly gave them the bad rep. Nowadays, without the altcoin flash and crash it's a very stable exchange.