I use the Arkel Commuter. They have many similar bags in their Urban/Commuting lineup, one of which will almost surely fill your needs. Most are available with an optional rain cover; I have one, but the bag's inherent water resistance means the cover only comes out during downpours, or when riding in the slop.

Arkel's products aren't cheap, but after a few years of regular use mine still looks and works like new. It's easy to see where my money went.