There is certainly a tension between these two concepts. They are not mutually exclusive, but it does seem that we have to take away from one to get more of the other.
We could probably have a greater degree of freedom from the fear of terrorism if we would do away with our civil liberties (assuming we spent enough money to let the government set up a really effective system). The government could do surveillance on suspect people and could minutely search anyone getting on an airplane or going near a federal building or other target (again, this would take huge amounts of money).
Alternatively, we could have more freedom. We could prevent the government from ever tapping our phones or using scanners to inspect our bodies before we board airplanes. This would probably make terrorist attacks more likely.
So, these two ideas are in some ways opposed to each other, even though we can have fairly high levels of both at the same time.