In addition, wouldn't Assad, the socialist, Baathist, secularist suspect any presence of Iran military and political operatives in his country to be a potential threat to his own regime?
No. Current events make this clear.
I think you've missed quite a bit of history here. For starters, Assad's not a Baathist, but an Alawite, a minor Islamic sect despised as deviants by both Sunni and Shia. Khomeini, ever the pragmatist, came to the aid of Bashir's father when his legitimacy as a Muslim and his somewhat secular values were questioned. Khomeni had the mullahs declare the Alawites legitimate members of the Shi'ite faith. In return, Syria helped Khomeini train terrorists in Lebanon, became the re-supply route for same, and regularly supplied Syrian passports to Khomeni's minions.
Nothing's changed since Bashar succeeded his father, except perhaps that the son is not very strong-willed (his father was a ruthless tyrant), and is more or less an Iranian sock puppet.
A marriage made in hell, in spite of the wishful thinking of our DOS and the NYT.