Ronald,
It plays both ways. If Assad is removed and the rebels seize control then Al Qaeda is not going to last long in Syria and certainly not hold any position of power. Only a proportion of rebels within Syria are Al Qaeda or the rest of the extremist nut jobs.
You only have to look at Iraq when Al-Q started pushing their luck and took over suburbs. That resulted in the the US and some insurgents combining forces and taking over those areas where Al Q had tried to set up controlled areas. Yes Al-Q are in Syria but you can't broad brush the majority of Assad opposition in the same light. Al Q and other extremists are always going to be in the background of such conflicts but they are never going to have majority popular support.