I am by no means an expert on Middle Eastern relations, however the Baath party was founded on pan-arabic ideas by Michel Aflaq. He was well aware that the population of Syria was in general reasonable religious, with some more than others. However their secular ideas, shouldn't be considered a declaration of war against Islam, but rather that the Baath party would operate on secular ideas in a religious state. As it is however the Muslim Brotherhood was banned throughout the Middle East for their dogmatic approach to Islam, and as such banned in Syria as well. The most dramatic confrontations between Baath and the Muslim Brotherhood happened in the early 80's, where the Muslim Brotherhood was deemed responsible for an assassination attempt on Hafez al-Assad. As such it came to open warfare between the Syrian regime, and the Muslim Brotherhood. However I reckon that as long as you were not a member of the Muslim Brotherhood, your personal beliefs would not be an issue, as long as you could accomodate the Baath regime.

Sources:

Dam, Nikolaus van (2013). The Struggle for Power in Syria: Politics and society under Asad and the Ba'th Party. 4. edition.