There are strongly conflicting reports on the Internet about the fate of the Christians in Homs. It is clear that many have left, specially in last February and March. But reports differ on now many and how they left.
On the numbers the figures differs quite a lot. Some report that Homs once contained 160,000 and that now about 1000 are remaining. Others that 50,000 have left and 1000 are remaining. Yet others that 90% of 80,000 have left. Mainstream media ignore the issue and most reporting is in religious publications.
Sources from the Syrian Orthodox Church report that: the city [Homs] has been emptied of almost 90% of its Christians. It is expected that a complete "cleansing" of buildings owned by Christians will occur within a matter of days or weeks by armed men from the Wahhabi "Faruq Brigade."
A source in the Orthodox metropolitan's office told al-Haqiqa that armed men from the Faruq Brigade went to the homes of the Christians, house by house, in the neighborhoods of Hamidiya and Bustan el-Diwan, informing them that they must immediately leave their homes and the city of Homs. [...] The church sources said that the armed men informed the owners of the homes before they departed that if they did not leave immediately they would be shot and pictures of their corpses would be sent to al-Jazeera with the message that the government had killed them. The source emphasized that all those who were expelled "were not allowed to take any of their possessions with them, not even extra clothes. Immediately after they left their homes, the buildings were occupied by armed men who considered it 'war-booty from the Christians!'" It should be noted that the Faruq Brigade is operated by armed elements from al-Qaeda and various Wahhabi groups and it includes mercenaries from Libya and Iraq. Last month they destroyed two churches with rocket fire, burning one and severely damaging the other.
However, the Roman Catholic Church, while first republishing the reports from the Orthodox, then came with reports from local clerics that the departure from Homs had been voluntary and due to the violence. Britain used this even as an argument to increase the aid to the rebels.
Interestingly more recently the Roman Catholic Fides came with a report about what looks like a clear case of ethnic cleansing: A disturbing news reaches Fides from the province of Hama, in the north of Homs: armed men have expelled all Christian families in the village of Al Borj Al Qastal, in the province of Hama. The news, spread by some international agency, is confirmed to Fides by local Church sources. The sources said that armed groups – of the militias of the composite Syrian Liberation Army - have penetrated into the village, driving out all Christian families, taking possession of homes and turning the Church in the area in military headquarters. The village of Al Borj Al Qastal is in the province of Hama, and welcomed about 10 Christian families, now displaced, innocent victims of conflict. (PA) (Agenzia Fides 12/5/2012)
So what is true? My guess is that the Orthodox and the Alawites are the primary targets for the rebels and seen as allies of Assad while the Roman Catholics are seen as a bit more connected to the West that supports the uprising.
Another factor that may play a role is follow-up cleansing. It has been reported that Baba Amr, the heavily contested quarter of Homs, has been largely deserted by its inhabitants. The question is where these people have gone. It wouldn't surprise me if they had gone elsewhere in the city and driven out people who they felt were connected with the regime in order to get a house. In this context one may remember that something similar was done in the early 1990s by Croats who had been driven from the Krajna by Serb separatists.
A third factor is hope for the future. Christians are afraid that painting this as a conflict between them and Sunni's will only further polarize the situation and lead to it that they will even more be targeted. Polarization might also make it more difficult to return once the conflict is over.
A fourth factor is that it is also official government policy not to publicly distinguish people by sect or religion.
Problem is that now even cities like Qusair - with 50% Christians - are targeted by the rebels and that the US is supporting them in that.
16 June 2012: This article ("Syrian Islamist opposition casts out Christians") tells that Christians in Qusair are forced to leave. David Enders of McClatchy claims that there is no persecution: The group also has been accused of targeting Christians in Homs. But interviews with Syrian Christian refugees who’d fled to Lebanon from Homs and Qusayr uncovered no evidence that Christians were targeted because of their religion. Rather, Christian refugees from Qusayr said that a Christian man and 16 others working with government security forces in Qusayr had been captured by Farouq fighters in March, prompting some Christians to flee. Members of Farouq confirmed the story, as well as the arrests..
26 June 2012: This article (Weeks spent with Syrian rebels reveal a force of Sunni Muslim civilians) mentions that Christians make up about 10 percent of Syria’s population. While they have participated in the demonstrations against Assad, they have preferred to flee rather than take up arms.. The article mentions that many people participate in the uprising because of family relations. Another article (Rebel-held town in northern Syria struggles to keep army out, avoid sectarian strife) tells how the uprising leads to rising tensions between ethnic groups.