While the courts have generally protected our individual freedoms, the American people tend to support the restriction of these rights in practice.
What reasons do you believe account for this fundamental difference of view?
I think pohnpei says it well in the answer above. I have a few things I'd like to add also.
The courts in this country are independent, that is, an independent judiciary, which is as the system was desgined by the Framers of the Constitution. While politicians have to react to what is popular with the people (or unpopular), the courts are insulated from popular opinion by the fact that at the federal level, they are lifetime appointments. In this manner, they can serve the function the office was designed for, to be an impartial judge on matters constitutional, as opposed to opinion polls and election cycles.
So they are able to protect individual freedoms more, sometimes, than the public would like because they can do so without fear of losing their jobs.
Secondly, the public tends to like more restrictions on individual freedoms of people they don't like, or they tend to favor order in general, as long as it doesn't restrict their own freedoms. Once their freedom is challenged, they usually quickly change their tune.
This question was asked and answered a couple of days ago. I am attaching the link to those answers. I want to add something to my answer from the other day, however.
I would say one reason for the difference is that people approve of individual freedoms in the abstract, but stop approving of them when they are used by unpopular minorities.
Here's what I mean by that. The freedom of religion, for example, is in the Constitution because people believe in general that they should have the right to worship as they like. But when people start worshipping in "weird" ways, the general public doesn't want to defend them. They want, instead, to take away their right to smoke marijuana as a religions rite or to have polygamous marriages.
So the rights are upheld by the courts (at times) because they are in the Constitution. They are in the Constitution because people approve of the rights in general. But people tend to support restrictions of those rights in practice because they do not like the ways in which the rights are being used by unpopular minorities.
Such a paradox occurs because we, as human beings, are not able to take the perspective of the universe-a completely neutral, objective point of view. When YOU want to practice your individual freedom, you think that you should be protected by law, because you're human, even if that certain action may disturb other people. For example, you would argue that you have the right to keep a dog as your pet, so you get one, even though your neighbors complain about the dog's barking. And you would argue that you have the freedom to keep a dog. However, if you are in the shoes of your neighbour, you would definitely argue that such a freedom should be restricted, because it harms other people.
Such a conflict on the extent of individual freedom would not ever occur if everyone had the ability to look beyond his or her personal desires.