From what I recall from a case study of the Supreme Court ruling, Chief Justice Rehnquist admitted that road checkpoints infringed on an individual's rights. However, he and the majority ruled that they are still justified because they are only minor infringements compared to the greater goal of protecting others.
If you ask me, this is proof that they are making "exemptions", if you will, to the Fourth Amendment. Sure, it seems somewhat minor and I could probably go around the checkpoint. That's a moot point, though. I tend to stand with the crowd who enjoy not giving up any of my rights.