Great title from the BBC. I'm not altogether happy about the stereotypical view of 'Puritans' here: the claim that they "looked down on drinking". They may have looked down on alehouses (the most basic type of establishment, which served only beer, and was the usual haunt of poorer customers), and have been concerned to regulate them, suppress disorderly establishments and act against excessive drinking, but that's not quite the same thing. They were perhaps more exercised than most about drinking on the Sabbath (worst of all, during divine service!), but this view of Puritans as anti-drink in opposition to revelling Royalists is crude. (The notion that coffee, or the coffee house, was in its early days a straightforwardly respectable alternative is also a bit off the mark.)
In fact, Parliamentarians from 1643 - like modern governments - had some reason to want people to be patronising alehouses and the somewhat more up-market taverns and inns, since that was the year that excise duties were introduced. Initially, they were intended as a temporary measure to raise revenue for the war. But the returning Royalists at the Restoration happily adopted this lucrative measure, and spent the next twenty-odd years trying to work out the most effective ways of collecting it. (Try government officials, farm it out, take it back under government control again...) Only after the Revolution of 1688 was the machinery really honed to become part of the tax system that funded British war-making during the eighteenth century. (The classic account of this is John Brewer's The sinews of power; for the period before 1688, C D Chandamon, The English public revenue). It wouldn't be too far out to say that our drinking (in part) funded the Empire... even though the customs and excise generated a massive smuggling industry.
Anyway, however, the article is quite right to point out that drinking could be a political act during the seventeenth century, and into the eighteenth. Especially the drinking of toasts. Now, disaffected Royalist gentlemen drinking toasts to the man they considered to be Charles II certainly was a problem for Interregnum authorities. After the Restoration, of course, the position was reversed and toasting the king was a statement of loyalty. And later, after 1688, there was a choice: between toasting the monarch or the Stuart pretenders. A man who refused to follow the lead of the company he was in could end up being beaten up. One who toasted the Stuarts too publicly could find himself in court on sedition charges (though not in a Tory-run county like Denbighshire where the greatest magnate, Watkyn Williams-Wynn, was strongly suspected of being a Jacobite sympathiser himself, and was rumoured to have had to make a hasty and undignified exit from Shrewsbury to avoid charges of drinking toasts to the Pretender).
Well into the eighteenth century, hard drinking was part of what it meant to be a gentleman; a 'six-bottle man' was a real man. What with all the claret and beef, no wonder so many of them had gout.
Update: The Guardian has also reported on this research. It also tends to emphasise the gruesome and sensational, but it seems a more subtle take than the BBC's version. But I'm just jealous now. Nobody ever came to me when there was a big story about violence in the news asking for rentaquotes about the seventeenth century...
There is a Chronology of English alcohol-related legislation at the lovely website The Pub in Literature: England's Altered State
Eighteenth-century drinking glasses has a wealth of information about the politics of drinking.
Jacobite rebellions gives a quick overview of Jacobitism.
And apparently it wasn't so very different in the American colonies...