Both the wiki entry and the FAS information on the Muslim Brotherhood points towards them being fairly fundamentalist in their take on Islam, although perhaps not to the degree of al-Qa'ida. Perhaps al-Qa'ida views them more as a threat to their recruiting pool than anything else, or something to keep destabilized in case they should get more organized. The wiki entry is especially interesting. Looks like they've been around for a good while, and seem to be able to "reproduce" themselves in a way similar to al-Qa'ida.

Information aside, I'm not sure exactly how you'd "use" a group like this. Depending on which faction you work with, some may be more willing to meet US interests halfway. It would involve some unpleasent pressure on some of our less acceptable 'allies' in the Middle East (such as the Saudis), but the return might be worth the risk.

http://en.wikipedia.org/wiki/Muslim_Brotherhood
http://www.fas.org/irp/world/para/mb.htm