Siege towers were not as vulnerable as you perceive.

 

With regards to projectile weapons: you have to remember that anything shooting at a siege tower has to be positioned on or in a wall or tower, which constrains the size of the device; and supplied with stone from within the besieged fortification, which constrains the size of the projectile. Also keep in mind that the framing and cladding of the tower would have been made out of heavy timber and not the dainty little pine 2"x4"s that often go into modern wooden construction.

 

With regards to incendiary weapons, you have to realize that popular culture drastically exaggerated the effectiveness of incendiary weapons available to ancient and medieval armies. Raw bitumen, pine tar, and lamp oil all burn fairly slowly and could be protected against by nailing wetted animal hides to the tower.

 

Lastly: the engineers building the towers didn't just randomly construct things to throw against the walls of a fortification. A siege tower could be defeated or delayed by moat, or even boggy, sloped, or uneven ground. The places where siege towers were most effective were places with badly flawed fortifications, and the engineers building these towers did so because they perceived these obvious weaknesses in design.