For better or worse Syria is still under the legal control of the Assad Government. ISIS may control large portions of the country but that does not extend to any airspace. Allied aircraft may not have the outright permission of the Syrian Government to operate in Syrian airspace but Assad is turning a blind eye because they are hitting ISIS. The Allies don't have the legal ability to deny the Syrian Air Force or anyone else access to Syrian airspace let alone forces invited into the country by the legitimate government.