I do. This is worth the extra effort and the fees to be honest because there are just so many exchanges that are closing down on a daily basis either from a runaway scam or a "hack". Even the best of them can't be trusted.
Cryptsy and Mt Gox were two of the most trusted exchanges but we all know how they ended up.
And now there's poloniex. I store a fraction of my altcoins on an exchange for ease of access, because it's indeed very annoying to have to sync all your altcoin wallets. But the rest i keep in my desktop wallets, especially bitcoin.