I've found CJ to be a lot of trial and error. Some advertisers perform well, some mediocre, and some not at all. I've at times sent thousands of clicks over big periods of time to advertisers that have not yielded a single commission. It can be painful.
I have a hard time comparing to AdSense because it took me awhile to get accepted, and now I'm still experimenting with it. Right now most of my revenues come from CJ. And yes, CTR for me is often below 0.01. It takes a lot of traffic to make money on that kind of CTR! But for better-targetted ads, I'm seeing higher CTRs. Banner placement, use of text links, these things also have big effects on CTR.