This is because the search is not being conducted for the purpose of conducting a criminal investigation. The court considers first whether the activity in question is done with a "reasonable expectation of privacy". Many things that look like a search, are not in fact searches for 4th Amendment purposes. This is because the activity does not carry the expectation of privacy under the circumstances.
It is a difficult analysis, and in all sincerity we should always be a check on the government's use of power. But the way to protect our liberty is by first protecting our very lives. We must elect good people if we are to be a free people. We must also be HEAVILY ARMED.
A strong constitution does not mean we have to be weak and vulnerable. I have to admit that my view of this issue has evolved (I hate that word) over the last 5 years. The danger is real, and it is more serious to me than my boring phone calls and e-mails being monitored. I don't know any other way to say it.
So those searches are OK because, when you come across the border or get on an airplane, you expect to be searched?