This made me concerned. I have my own domain which indeed uses Google Apps, but I just forward all my mails from there to my @gmail.com account. This needs to switch.
Google owning your data is not the problem here, while you can backup it. The real problem is them owning your identity.
What if your domain registrar simply fails and loses your records?
The US government has been seizing domains associated with sites accused of violating laws; are you with a registrar who will fight that?
I'm not saying that you shouldn't own the domain for your email address--it's simply that you should realize that it solves one problem but creates others.
Once you look at things at detail, almost everything in your life is dependent on trust. Knowing how much to trust different aspects and how to evaluate risks is key.