With a budget of $1000 you can buy a really nice hybrid. The Trek FX series bikes are pretty popular here. In your price range (assuming a bit of discount) you are looking at the FX 7.4 or 7.5. The 7.5 looks quite similar to the 7.4 and you are probably getting better components with the 7.5. The other noticeable difference is the 7.4 has 32mm tires, the 7.5 has 28mm, which are probably narrower than you want. I do not know if the 7.5 will take 35mm tires. The store is usually willing to swap out tires for no/little cost. Also, the 7.4 has triple chainrings on the front, while the 7.5 has a double. Both are 9 speeds and both have carbon forks. The Sirrus Elite (or Elite w/Disc) are in your price range. The Elite looks very similar to the 7.4: triple, carbon fork, but 28mm tires (not sure how wide a tire the bike will accept). The similar Giant model is the Escape 0, which is a 10 speed, carbon fork, 32mm wheels. Cannondale has the Quick, the SL3 looks like it is similar to the other bikes and it has 32mm tires. The Jamis Coda Comp is the Jamis version; note that Jamis bikes are steel while all the others are aluminum. I don't think frame material matters that much unless you live in a rain forest and need to worry about rust.
All of these bikes should accept fenders, but be aware that fenders might limit the size of tire that can be used.
I think if you go to the bike stores and say "I want to see what bikes you have in the $800-1000 price range", you'll see all of these bikes. They are very similar. Look for last year or 2011 models to save yourself some coin. Test ride bikes and you'll find some that you like, others you don't. Remember that fit is key.
Report back :-)