While this is true, I think that some historical perspective will be helpful here. As Leland Ryken stated in his book, Worldly Saints, the Puritans As They Really Were...My understanding is that the Geneva version was popular even after the 1611 KJV, but I believe by the time of the Westminster Assembly the KJV had gained general approval in Puritan circles. The Westminster documents, I think -- including the Bible version used in conjunction with the Annotations -- all quote the KJV. So I think it depends on which timeframe one is speaking of. The Westminster Puritans, I believe, primarily used the KJV.
It is also to be noted that the Geneva Bible, more than any other, contributed to the King James Bible of 1611. At the Hampton Court Conference (January 1604), it was the Puritans who made a number of proposals to King James, among them being the suggestion that the work of a new translation be initiated. This proposal was moved by John Reynolds, who was the president of one of the colleges of Oxford, and a prominent leader of the the Puritan side of the Church of England. King James was no friend to the Puritans, and at the same conference remarked, "I could never yet see a Bible well translated in English; but I think that, of all, that of Geneva is the worst.""If we are looking for a specifically Puritan contribution to Bible translation, we should look to the Geneva Bible of 1560. Produced by the English-speaking colony in Calvin's Geneva, it became the favorite Bible for several generations of Puritans, as well as the Bible used by Shakespeare and Spenser. It was printed with marginal notes containing Puritan and Calvinistic interpretations of passages. Of the more long-term importance were several innovations that set the standard for future English Bibles." p. 138.
Thus, to spite the Puritans, King James set up a committee of fifty-four scholars who did the translation work, which was evenly divided between Anglican and Puritan parties. The irony is that they used more from the Geneva Bible than any other version to help them with their translation work.