Update from Thule
After reading every post in this thread I contacted Thule to find out why they haven't made a rack for the Sonic. I asked the customer service rep to get an answer from an engineer. The answer that was given to me was that it was because the Sonic wasn't expected to sell enough to justify making a rack for it. I asked specifically about the hard-to-fit door frame. As of this date, Thule is denying that that's the reason why they're not making a rack for the Sonic.
If you read this whole thread closely you will find a confusing array of contradictory statements about various racks. One reader read all the posts and concluded that the only safe rack would be one that is permanently screwed into the roof. And yet, someone else posted that he drove from Arizona to Alaska with the GM OEM rack and had no problems, which means perhaps there IS a safe clamp-on rack for the Sonic.
A canoist pointed out that there is only 28" between the bars on the GM rack, and this distance is not adjustable because the feet must be placed in specific indentations in the car frame. Actually 28" is considered a safe distance between the bars for transporting a kayak or canoe, with the caveat that canoes and kayaks should always be secured with bow and stern lines regardless of the space between the bars. I do think there are potential problems with loading a kayak facing deck up on saddles, because the straps may pass over the coaming, which is a weak area. I can also understand why someone with an 18' canoe might think 28" isn't idea.
Important: The indentations in the car frame for the rack feet push the racks very far forward. If you load your canoe or kayak from the rear, you will have to clear the spoiler and a couple of feet of roof before you get to the rear bar. This could be a real problem for some people as you will need to figure out how to protect the spoiler and the roof. Another option is to load your kayak or canoe from the side, which is not without its pitfalls.
I concluded after reading this entire thread and looking at a lot of racks that although tracks screwed into the roof might be the safest, they're not the most practical solution and they're expensive because you have to add to the tracks the cost of the whole Thule or Yakima setup and possibly installation, which could run up close to $800. Then there's the question of who will do the installation. Two GM dealers and an auto body shop refused to install tracks on my Sonic because of the risk of hitting an airbag curtain or wires in the roof. Companies that make tracks insist that they're easy to install, but I had no luck convincing someone to do it and it's not something I want to do myself.
It's really unfortunate that Chevrolet (a) made such an odd door and frame and (b) put the rack indentations where they are. I think the Sonic appeals to a lot of outdoor people who appreciate the cargo space with the rear seat folded down. Those folks need a roof rack for outdoor gear like kayaks. Lesson learned: I will never again buy a car without first checking to make sure there's a Thule rack that fits it off the shelf. It just never occurred to me that it could be this difficult to find a safe roof rack. For me the roof rack is as important as any other part of the car.
In sum, there are some allegations in this thread that are now denied by Thule and that imply that the door and frame on the Sonic are so unsafe that no clamp-on rack could be made for it, along with an allegation that GM went to some cheap Korean company, implying that the GM rack is unsafe. The thinking is, "If Thule couldn't make a safe rack, then no one can and therefore the GM rack is unsafe." If anyone has actual proof of these things it would be good to hear it. If anyone has actually had a GM rack fall off their car, it would be good to know that as well. If those allegations are not true, it might not be good to encourage people to drill holes in their car if the GM rack is actually safe.
I decided to go with the GM rack knowing its faults because I just can't afford to spend $500 to $800 on a rack setup every time I buy a new car and I don't want to drill holes in my roof. I'll report back on the results.