I disagree. If you think the government is trampling on the civil liberties of someone, it matters, whether it is one person or 50 million people.
In this case, I think the question is, is the government actually trampling on the civil liberties of anyone by requiring that health insurance companies cover all preventative care (including contraceptives) without charging a copay.
I would answer no to that question.
The government is setting a regulation for a business (health insurers). Anyone who has a moral objection to contraceptives is still free to not take contraceptives.