I am a pro-choice atheist. But I support a regulation, recently promulgated by the Bush administration, that would cut federal funding to nearly 600,000 hospitals, clinics, health plans, doctors' offices and other entities if they do not allow their employees to opt out of providing certain types of care -- including abortion services -- on grounds of conscience and personal belief.
Ask yourself: What are some of the bad things that have happened because people refused, on conscientious grounds, to do what the institutions in which they were embedded demanded? Now ask yourself: What are some of the bad things that have happened because people overcame serious qualms and did what they were ordered to do?
The idea that we must respect individual conscience as a moral arbiter is a fundamental insight of the Protestant Reformation and of the American individualism of such figures as Emerson and Thoreau. It is at the core of our traditions and our freedoms. This idea means nothing if we respect it when we agree with its results and not when we don't.
He does a good job, I think, of pointing out the importance of respecting individual conscience. I'd recommend reading the entire article.