I keep all my domains and hosting seperately and strongly recommend the sam because you never know what can happen with your hosting provider in future.
Keep them separate, but if you register your domain with a reputable host then you shouldn't have anything to worry about.
All my domains and servers are separated. I don't trust these hosting company's, who giving free domain. I don't have then full control over my domain. And second - I have lot of domains - its cheaper me to register them directly and handle them. I can easy change nameservers and point to new server etc.