No, USB isn't better than CF. And CF isn't necessarily better than USB. They're just different. *Name brand* flash is probably better than generic flash, especially if it comes from a company that has a reputation for quality and reliability in memory products.
One edge for CF is probably that you're less likely to inadvertently yank out a CF card, especially if it's buried in the machine. USB thumb drives are a little scary that way. However, some boards have internal arrangements for internal USB storage.
Another edge for CF might be that it tends to be slightly older tech, and may be a bit more reliable. I believe the primary use these days is by pro photographers, who typically don't like it if they lose stuff, and so there may be a bit of bias towards better components, etc.
The problem is that CF is a bit hard to leverage on modern computers - you may not be able to go to the corner computer store and make that happen.