I have found the same thing. I put a half scoop of soy protein powder on my granola in the morning, and after a 2 or more hour ride often have a recovery drink made from OJ and whey protein. The small amount of protein before a ride seems to make the fuel last longer, and the protein and carbs after help recovery.

There's quite a bit of research showing that protein with your post ride carbs helps to speed glycogen storage. That is useful if you are doing another long/hard ride the next day. (this is where the highly marketed 3:1 ratio comes from although other ratios work as well). I also think that the shot of protein helps muscle recovery.