For the most part, yes, quick-release wheels are safe to use. Then again, it does come down to how you are using them. For the record, quick-release wheels make it much easier to remove the wheels on your bike when you need to. This can come in handy when you want to transport your bike, as an example.
But, because the quick releases will be holding your wheels in place, you need to understand how to use them properly. In other words, you can be your own worst enemy here.