Though the dog may be tossed against the side of its crate during an accident, the chance of serious injury is actually pretty small. The dog may end up a little bruised and sore but otherwise okay. The big advantage to a crate is that they are contained, so after they accident there is no worry about them getting loose and getting injured or killed by another car. Even if the dog is normally fine with their seatbelt harness, if you are injured and perhaps even unconscious, would your dog who will probably be quite fearful at that point stay in the harness?
It is true that my boy Nicky has always had issues with his crate. Even at 10 1/2 years old he still does not like being crated alone. He will happily get in his crate in the car though and sleeps during the ride. He will occassionally whine when we are on surface streets but not too often anymore. Our first few trips with him in the car were quite traumatic for all of us, he would scream and pitch a fit for the whole ride, even the whole 2 hour trip to Dillon's Beach the second weekend we had him. He did pretty quickly learn that 99% of the time we were going someplace really fun and calmed down considerably.