Do you really think they have a blind suspicion of everyone? The vast majority will go through with minimal questioning, and these types of questions try to tease out suspicious behavior. I don't think it's a "you are guilty by default" type situation.
How would you rather the border patrol act? Keep in mind there are various types of illicit behavior that are not desired within society--this is a fairly inevasive method all things considered.
Isn't being suspicious of everyone the rational response? You see thousands of people per year and your entire job is to identify the few who are doing something wrong (smuggling, using a false passport, whatever).
If you're not going to be suspicious of everyone, which subset of them should you be suspicious of?