In my opinion , yes they are safe but I can't say that they are at 100% safe level because they are only exchange and if you will have  to access your account then surely you will needed to give email id and password and as we know that in the present time it is not much tedious for a hacker to access your email id and also your password by reset .
And second thing that there can be vulnerability in the programming of the exchange , and also there are even beside this many ways to inject Thier program to ACCESS the exchange , so here we can't say theya are safe .
Here I don't mean that they are fully unsafe , but here you need to remain clear in your mind that exchange are not just toys , they are improving theirself time to time with better updation by Thier team developers , a simple example we can have is yobit , since many people says that yobit is scam exchange but it was hacked by hackers once but now it is fully protected and a small activity ( about attack over the site ) they block every transaction for withdrawal .
And that why I didn't found anything bad in this thing , that we should have our altcoins at exchange , they are 99.99% safe .
But if you are willing to hold your altcoins assets for long term of one to two years then it will be better to use official wallets and take backup of your wallet for sure safety .