I think CPM is more important than CTR (although most of the time they are directly proportional ). If most of your traffic if from social networking sites than CTR will be low. Search engine traffic are know to produce high CTR. Check your stats and see where your visitors are coming from .
I used to get awful conversion rate until I decided to experiment and play around with ads positioning and placement. Main thing is that you must give time to see and monitor the results before moving on to next plan. Placement is very important and you should aim for at least 2-3%
Play with placing and units until you reach at a better CTR. I always do this for my sites when I notice a low CTR. But generally, 2% and more is good.
In text ads like infolink and kontera get 10-15% easy banner ads are often below 10%, blogs below 5%, and forums get below 2% normally.