That said, the 0.01 transaction fees are a relatively new feature, and since they were introduced so quickly, they should have been reversed to 0.0005 equally quickly in my opinion.
Don't know what version of bitcoind and OS are they running, the latest builds nags if they're using Debian 5 for an instance, so their fee may still be 0.01.
Anyway, CPU mining is inefficient and can't compete with GPU mining. So any possible earnings of CPU mining pools will be small.