Riding a Subway isn't a right, it's a priviledge, you want to ride, get searched. Just like an airport.
Where you have a large congregation of people in a small area, I would feel much safer to have these searches than not.
Sorry you feel violated, maybe you have something to hide?
Your fredoms have not been violated in anyway for the search. What right was taken away? Nothing. And if you are embarrassed about the contents in your bags, perhaps they need to be left at home.
What do you mean by priviledge? Are there other privileges, like, say, gun ownership, that the government is empowered by our Constituution to restrict?