The thing is, the protest movement is actually against the Ayatollah.
Ahmadenijad/ Mousavi are just symbols for them to rally around. Because Ahmadenijad is backed by the Ayatollah and the IRGC (military leadership), protests against Ahmadenijad are also protests against the whole power structure.
Interestingly enough, the head of the Guardian Council which has the power to appoint/dismiss the Ayatollah is backing Mousavi. But he has been denounced by Ahmadenijad and his family members have been detained by the IRGC, which leads some to believe that, rather than accept their candidates electoral loss, the IRGC has staged what is essentially a military coup.