From Chapter 2:
But the apothecaries were the most usual salesmen, and their shops and the ordinaries were the customary day meeting-places for the more fashionable smokers. The taverns and inns, however, were also filled with smoke, and taverns were frequented by men of all social grades. Dekker speaks of the gallant leaving the tavern at night when "the spirit of wine and tobacco walkes" in his train. On the occasion of the accession of James I, 1603, when London was given up to rejoicing and revelry, we are told that "tobacconists [i.e. smokers] filled up whole Tavernes."

From Chapter 5:
The belief in the prophylactic power of tobacco was, however, very generally held. When Mr. Samuel Pepys on June 7, 1665, for the first time saw several houses marked with the ominous red cross, and the words "Lord, have mercy upon us" chalked upon the doors, he felt so ill at ease that he was obliged to buy some roll tobacco to smell and chew. There is nothing to show that Pepys even smoked, which considering his proficiency in the arts of good-fellowship, is perhaps a little surprising. Defoe, in his fictitious but graphic "Journal of the Plague Year in London," says that the sexton of one of the London parishes, who personally handled a large number of the victims, never had the distemper at all, but lived about twenty years after it, and was sexton of the parish to the time of his death. This man, according to Defoe, "never used any preservative against the infection other than holding garlic and rue in his mouth, and smoking tobacco."