Because in these brutal internecine conflicts in Arab countries, there are never any factions that are simply good guys. Because Islamist elements among the "Syrian rebels" are already perpetrating severe persecution of Christians in Syria, who by and large haven't joined this revolt and fear the demise of what they consider the relatively tolerant Assad regime. (There are indeed elements of Christianity in the Alawite religion and Alawites don't seem to have any special animus toward Christians.) Because Islamist elements have a considerable role among the rebels and it's a real possibility that they'll become dominant (as in Egypt, Libya, and Tunisia) if the rebels succeed to overthrow Assad. See Frank Crimi's eye-opening article.
The Assad regime's committing atrocities? No doubt about it. Like I said, there are no good guys. From Israel's standpoint, Assad is a terror-supporter and major component of Iran's axis. But he's kept the Israeli-Syrian border quiet. His replacements could be worse.