Because from Sesshoumaru's point of view, could the Transports have done a better job in finding a place to take everyone as the world was sent to Hell in a Handbasket? Probably not.

But is he thrilled with the Initiative? Hell no. They took him from his home twice for this war, so he has no love for them. He's told them before this is a human problem, humans can deal with it.

However, there are a few he will protect, so if they are harmed, there will be a very angry demon to contend with.