I have to support Pohnpei's post as well. Homeland Security can infringe on the rights of people (seemingly at any time they wish based upon any aspect which may set off a "red flag"). I think that there are definite points where the two cannot exist at the same time.
I'm assuming by the phrasing "civil liberties" what you mean are Rights. By "homeland security" I assume you mean the country's security. The purpose of government is to safeguard Rights, and every individual in the US has a Right of security.
But they also have a Right of privacy. The question is how much and individual can exercise his or her Right to privacy when the Right of security is threatened. There are not opposing concepts, and one does not preclude the other; the challenge is to get the delicate balance between these Rights correct.
Pohnpei's response is excellent. I would simply add that without sufficient homeland security, civil liberties could be severely curtailed for a number of reasons. For instance, if a terrorist group ever succeeded in setting off an atomic bomb in the U. S., there is no telling what kinds of emergency measures would be imposed. So far, the government seems to be doing a reasonable job of mantaining civil liberties while also protecting homeland security.
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.