It actually makes perfect sense. For Saddam the Shia, and for Assad the Sunnis, were the group that were an actual risk to him.
So they had every incentive to go easy on groups other than their main threats fir whatever support they could get from them against their main threats.
Unfortunately, this means that when the dictator is overthrown the minority groups he “favored” are seen by the majority as collaborators, whether they in fact were or not.
I understand your logic trail. If Christians didn’t come out in favor of Assad for instance though, it wouldn’t seem the next crew would go after them based on their support of him.
I would still lean toward it being radical Islamic thugs and the elimination of anything not Islamic in their nation.