Sectarian chauvinism certainly exists and is present in all sects and is not limited to wild-eyed salafists. However, relations among the sects in Syria have been generally good, a situation that antedates the Assads. Moreover, I strongly believe that the primacy of sectarian loyalties is diminishing with time. At independence, it was difficult for people brought together within boundaries drawn by colonial powers to feel like citizens of a nation. Loyalties were first and foremost regional, religious or tribal. However, after sixty years of common history and common shared memory, even the citizens of the most artificially drawn up nation develop a sense of a shared identity. That is why the current generation of young Arabs identify themselves first as citizens of their respective countries. We saw that feeling clearly manifested in the demonstrations in Egypt and we see it now among the young Syrian protesters. Even in the country where sectarianism is institutionalized, Lebanon, young protesters have been out in the streets demanding an end to the sectarian sate.
The Syrian regime is currently pandering to the fears of minority communities. They in turn, are understandably nervous. However, the best way to insure the rights of minorities is to have those rights protected by a representative and responsive government and not dependent on the benevolence of an authoritarian ruler.