I guess most bags today have a rain cover, my lowepro does.
I advice you to check out some store or internet based store for bags, and look if you find something that suits your needs, and see if the specs tell that it is rain proof.
My decision for a bag for my D90 became the Lowepro Flipside 200, that is a lightweight backpack with a lot of good features. Check out my review of it here at the forum: http://www.cameralabs.com/forum/viewtopic.php?t=12885
If this doesn't seem like something for you, I strongly recommend you to check out other lowepro products, as the quality is great! [/url]