I have alot of algae growth, but I try to ignore it. I have heard that to prevent it from growing you can add a couple of drops of Physan 20 to the water, every time you water, from as soon as you pot the plant to the time it dies. That's too much work for me. You can also use dark pots to cover the outside of the clear ones to prevent light from reaching the algae.
Like I said, I just ignore it. If centipedes and roly-poly's don't harm roots, algae shouldn't either.