They're simply not tough enough. Last night in Siege, ONE level 70 rogue managed to take down one of our gates very quickly, then run inside to hide. He then proceeded to kill buildings when no one was around. ONE player shouldn't be able to take down a gate that easily, regardless of how good his gear is. As Siege War currently stands, siege weapons are pretty useless unless you're too low level to attack gates & buildings. Most sieges never involve siege weapons at all, but siege weapons like rams & catapults are what players should be using on gates.
So what I would suggest:
1. Decrease the amount of damage that player based attacks do on gates.
2. Increase the amount of damage that siege weapons do to gates & buildings to encourage guilds to build & utilize siege weapons.