Some of the Rebels are extremist Muslims. The rebels aren't a monolithic, united organization like the Western Media wants you to believe. There are some rebels who are a part of the larger, better organized rebel force, but there are a lot of rebels out there who are extremist Muslims and probably want to wipe out not just the Alawites, but the Christians & Jews as well.
On the other hand, the Assad regime is also corrupt, and would probably have had no qualms about killing Christians who are "in the way". The Christians in Syria are stuck between a rock & a hard place.
The conflict in Syria, unlike what western media tells us, is definitely sectarian violence between Muslims. It is basically a conflict within Islam more than it is a Syrian political conflict.