The situation in the Middle East is more complicated than this article alludes too.
Firstly, contrary to Assadist propaganda, Western Orientalism and social prejudice. Not all the rebels are Islamists.
Secondly, the Islamist groups are varied in terms of ideology, affiliation and general discourse. One faction of the Islamist rebels are Al-Qaeda aligned and they display complete hatred to all minorities (the fear is not entirely unfounded).
However, other Islamist factions are not Al-Qaeda aligned and do not have an antagonistic and belligerent attitude towards minorities. A good case in point is what happened in the Christian town of Maloula.
Maloula is an old Christian town with two large churches, including one church which pre-dates both the Vatican and Christianity in Europe. I forget what this church is called, but it's known as the refuge, because during Roman rule of Syria, Christians would hide in the secretly built basement of the Church from Romans who wanted to kill them. It is also one of the few places in the world with Aramaic is spoken (the ancient language of Jesus Christ).
In September, when the Syrian regime thought that the Americans were about to attack, they decided to withdraw their forces from the Christian town. They had hoped that Islamist rebels would enter the town and massacre the residences- so that they could embarrass and dissuade the United States from attacking.
However, this tactic failed, because the Islamist who entered were not the Al-Qaeda aligned group. When they entered they were greeted by the local nuns and they promised the nuns that they would not attack the local population. They claimed that the Christians were their brothers and sisters and that they were only interested in regime soldiers.
The Christian residence ended up helping the rebels. Treating their wounded, feeding them, clothing them and sheltering them. When the regime founded out their tactic had failed, they then surrounded the town and threatened to attack. The Islamist rebels decided to leave the town before any assault and they told the locals they did so to avoid local Christians from being harmed.
So the picture is more complex than that. However, much of the sectarianism, which does exist comes from the regime. Using minorities is how the regime in Syria survives. Some of the hatred for Christians by some of the Sunni Muslim rebels steams from the belief that they are close to the regime and thus complicit. But it has very little to do with actual religious difference.
Keep in mind between 125, 000- 200, 000 people have been killed in Syria, another 2.5 million are refugees and 3 to 4 million are internally displaced. And most of them are Sunni Muslims, thus if we to sectarianise the figures, Sunni Muslims have been the overwhelming victims of the conflict.