Plants grow aerial roots because plants like to grow aerial roots. Stem plants, especially, grow them no matter what the water is like. You can either learn to like them or keep pruning and tossing the bottoms while replanting the tops.
I have in the past just cut the roots off as close to the stim as possible and have seen no difference in the plants. They just regrow the roots. Now my tank it so full of plants that I guess Im getting used to seeing the roots or they just blend in better.