In the early days of our republic, federal excise tax on tobacco and spirits comprised nearly all of the nation's internal revenue.
Well, then they weren't modern libertarians. That doesn't mean that there isn't an issue about the government and its relationship to personal freedoms.
Or, if the tax is low enough so that it doesn't interfere with behavior, then why shouldn't it be more broadly based so that we all help pick up the tab, and not only one subsection of society?
This seems like an argument for a flat income tax or the so-called fair tax (across the board national sales tax.)
Not at all. We can all help pick up the tab, but in a progressive manner. Broad-based does not mean flat; it just means that everyone (or everyone above a certain minimum threshold) should contribute something.
And I think that's a key problem with our politics today. It's too easy to be in favor of something (like expanding health insurance for children, or wars) as long as someone else picks up the tab (like smokers, or the next generation of taxpayers). Government is supposed to be the means by which we tax ourselves for the programs we say we want. If we're not willing to contribute, maybe we should admit we don't think the goal is that important. But we can't have it both ways indefinitely. (And that goes for tax cuts without giving up programs, too.)