Now that the Supreme Court has ruled to uphold the PPCA, a fruitful discussion about government mandates should be more possible without immediate worries of whether gettting it 'wrong' hurts your own side or helps the other side of whichever political divide you happen to be on.
I tend to buy into many of the libertarian arguments against mandates--that the government should generally minimize its decisions about how citizens live their lives. But an anti-mandate stance has virtues even to those who don't agree with the libertarian critique.
Government mandates tend to undermine the democratic balance between government action and conscientious objection. In most modern democratic-style states, we allow for tolerance of moral disagreement by separating taxing and spending. For the most part, everyone gets taxed and the money goes into a government pool. That pool of money becomes the government's money. There are then various government means for determining how that money is spent (direct acts of the legislature, funding through various agencies, etc.). Nearly everyone has some disagreement with some of the choices made. Sometimes that agreement has specific and strong moral dimensions (you may believe that the death penalty, or abortion, or crack vs. powder cocaine sentencing disparities are injustices). You are certainly free to use the political process to attempt to change those government allocations. But the process allows for some moral distance. You disagree with how the government is spending its money. You want to use politics to change how the government is spending its money. But you aren't generally forced to participate in whatever it is that you object to more than the fact that you have been taxed, and the government later decided what to do with the tax money it collected. Systemically this allows for diversity and tolerance for many of those who lose out in the political system. You lost out on your opinion about the death penalty? Fine, but we don't force you to pull the switch on a murderer.
Government mandates raise the stakes because they don't allow for that distancing. They force moral dissenters to choose between personally engaging in the activity in which they lost the political fight, or to defy the government and break the law by violating the mandate. Even in non conscientious objector cases, government mandates force dissenters to directly participate in the activity that they just lost a political fight over. It is something worth thinking about when there are non-mandate options.