The problem of low CTR can sometimes be concerned not only with your ads optimization, but also with your niche. For example, this blog has higher than average CTR, and i'm sure i haven't reached it's potentional yet, but i have a blog dedicated to free mp3 downloads, with the same layout and ads placement, and it's CTR is still okay, but about 3 times lower.
It's easy to understand - people looking for free music have no reasons to click advertising, but those who are going to buy tickets or CDs or equipment can certainly do so.
So if you're comparing your CTR, be sure that you're checking resources from the same niche. And choosing a niche topic be sure, that people interested in it are likely to spend money.
These days i'll make one more post on high / low CTR niches, so do not forget to bookmark this blog!