You got it backward. Al-Qaeda is fighting for us. Just like they did against the Russians in the 80's and the Serbs in the 90's. And as well they should since its US taxpayers that are giving them financing, training, weapons, logistical support, air cover, intelligence, command and control, and "advisers" on the ground. They are aren't even finished with the Libyans and already Al-Qaeda is attacking the Syrians so we have a convenient excuse to topple that government.
Al Qaeda (Sunni) was never well liked in Iran (Shia) and we even got some support from Iran in western Afghanistan for a while. Iran has been giving us a hard time in Iraq because the minority Sunni used to rule the majority Shia. In Bharein the majority Shia are ruled by the minority Sunni who are being helped by the Sunni Saudis. Iran will not be happy that Syria’s Alawi (Shia sub group) government is likely to fall to Sunnis.
If you wish to better understand the violent crosscurrents of the Middle East, study the history of Europe in the 2 to 3 hundred year after Martin Luther began the Protestant Reformation.