From Chapter 1:
It may further be added that though the use of tobacco was known and practised on the continent of Europe for some time before smoking became common in England—it was taken to Spain from Mexico by a physician about 1560, and Jean Nicot about the same time sent tobacco seeds to France—yet such use was exclusively for medicinal purposes. The smoking of tobacco in England seems from the first to have been much more a matter of pleasure than of hygiene.

From Chapter 5:
Among the many medicinal virtues attributed to tobacco was its supposed value as a preservative from contagion at times of plague. Hearne, the antiquary, writing early in 1721, said that he had been told that in the Great Plague of London of 1665 none of those who kept tobacconists' shops suffered from it, and this belief no doubt enhanced the medical reputation of the weed. I have also seen it stated that during the cholera epidemics of 1831, 1849, and 1866 not one London tobacconist died from that disease; but good authority for the statement seems to be lacking. Hutton, in his "History of Derby," says that when that town was visited by the plague in 1665, that at the "Headless-cross ... the market-people, having their mouths primed with tobacco as a preservative, brought their provisions.... It was observed, that this cruel affliction never attempted the premises of a tobacconist, a tanner or a shoemaker." Whatever ground there may have been for the belief in the prophylactic effect of smoking, there can be no doubt that in the seventeenth century it was firmly held. Howell in one of his "Familiar Letters" dated January 1, 1646, says that the smoke of tobacco is "one of the wholesomest sents that is against all contagious airs, for it overmasters all other smells, as King James they say found true, when being once a hunting, a showr of rain drave him into a Pigsty for shelter, wher he caus'd a pipe full to Be taken of purpose." But here Mr. Howell is certainly drawing the long-bow. One cannot imagine the author of the "Counterblaste" countenancing the use of tobacco under any circumstances.