You are certainly more knowledgeable about this than I, does Syria even have the capabilities? Could they be getting assistance from another country in the ME?
Cruise missiles are subsonic, but they hug the terrain on approach. It’s not impossible to intercept them, because they were, along with an F-117, over Bosnia in 1999. When a target is at low altitude or has low observability, having defenses properly emplaced can lock on it. Stealth aircraft aren’t ‘invisible’ to radar - they just have greatly diminished radar signatures. The same is true for an 18ft cruise missile flying low. If you have a group of radars and SAM systems looking the right way, the target can be triangulated and locked on through shared information on a networked defense system.
It requires a good crew with quick coordination. I doubt the Syrians have more than a few really good crews and they would be responsible for protecting Assad and their most important areas. They may have been able to get a Tomahawk or two, but nothing near what they’re saying.