Sorry to hear about your issue with them but I have to add they are my most trusted exchange for alts, bittrex not that far behind. With poloniex your funds are safe they do seem to have problems with depositing and withdrawing some coins but you know your funds are safe. I notice the first time I had a problem I wrote multiple messages threw frustration and that was the longest they have ever took. It will get sorted soon enough, probably already is?
They might be safer than other exchanges out there but it's a bit of a stretch to say that funds kept with them are guaranteed to be safe. Many exchanges can and have been hacked in the past, and Poloniex isn't immune to this. The only true safe solution to storing funds IMO is keeping your coins locally on your computer (and preferably in cold storage) or in the form of paper wallets.
Exchanges are more or less a necessary evil though. Despite being a generally unsafe place to store your funds, they are necessary for exchanging between coins. By setting up deposits and withdrawals immediately before and after trading and not keeping your coins stored there for any longer than necessary, you can reduce (but not completely eliminate) your exposure to the risk of them getting hacked or running off with your funds (the second one is probably not a huge risk in Poloniex's case but it's definitely a major problem with shadier exchanges).