Mubarak regime needs Muslim Brothers public and secret organization to scare the West , the US and even the civil secular trends in Egypt. Muslim Brothers are Mubarak’s excuse to stay in power. As he may say: Who is better: me or them? The answer is: You are bad but they are the worst.
Another reason is he needs badly the Wahhabi Muslim Brother culture instead of culture of democracy and human rights. That is why he persecutes the Quranist peaceful Muslim scholars. The Quranists prove the contradiction between Islam and the Sunni Wahhabism. This will destroy the Wahhabism if the Quranist scholars are protected and supported. However, in spite of being poor and helpless they are so successful in war of ideas against Wahhabism and the Saudi influence and Mubarak regime that the only way their enemies have is persecuting them.