I am not saying those guys were saints by any means but I don't recall any programs by Mubarak/Assad/Saddam to exterminate Christians.
Saddam gassed the Kurds and Assad's father and uncle massacred thousands in the 80's. Assad (current) was also a huge net exporter of terrorism who supported groups like Amal, Hezbollah, Hamas, the PKK, and even Al Qaeda in Iraq. Now the ISI and the Kurds have turned against Assad during the civil war, but that shouldn't cause us to forget his previous stances, and right now he sponsors the mass killings of Sunnis in Western Syria via armed militia groups. It is the bloodiest current sectarian cleansing in the entire country.
What people like Assad do during civil war is purposely stoke ethnic and / or sectarian tensions in order to garner support for themselves and / or justify their own actions. Assad has done this routinely and always emphasizes the Islamist nature of the "rebels" even though many FSA brigades are secular in their political orientation. He overplays groups like Al Qaeda on purpose.
Lately the ISI(S) hasn't even been very active in fighting Assad and seems to be more interested in establishing its own zone of control in the north and attempting to co-opt Al Nusra. Most of the current major fronts are controlled by more secular groups (Homs, Damascus, etc). Now granted, the FSA does have some Islamist groups supporting it, but they are the exception rather than the rule and aren't linked to Al Qaeda.
Rebels often try to promote sectarianism for their own purposes too, and that is a major tactic of the ISI as can be seen in Iraq (used as a political tool to undermine established administrations).
But we see the same tactics in other countries too even in the absence of religious sectarianism; instead it is ethnicity as is often played in the DRC and was especially strongly used when Mobutu Sese Seko was in power and in Kabila's early years.
Sectarianism helps them out, so they run with it and emphasize it.
