I took a course in college that, in part, dealt with this issue. The professor for that course, Maria Boes, wrote an essay titled "On trial for sodomy in early modern Germany."

Boes notes that the early modern period saw a significant increase in prosecution of homosexuals throughout Europe, and that "by the mid sixteenth century same-sex relations had become criminal in most European areas." Her essay, however, deals specifically with the city of Frankfurt am Main, which had only two sentences for sodomy from 1562-1696 - far fewer than in cities like Venice and Florence. This suggests that legal persecution of homosexuals was not uniform throughout Europe during this period.

Boes points to religion as the cause of the rise in legal proceedings, noting that the Catholic Church had suggested a punishment of death by fire as far back as the Council of Nablus in 1120. Perhaps this explains why Frankfurt am Main sentenced far fewer men for sodomy, as it was dominated religiously by Lutheranism.

This essay is part of a collection, which is titled Sodomy in early modern Europe, edited by Tom Betteridge. I cannot speak to the other essays - which cover areas including England, Scotland, Venice, and Geneva - as I have not read them. But I would encourage you to check it out for yourself.

URL here: http://www.worldcat.org/title/sodomy-in-early-modern-europe/oclc/50102063

Edited for non-Amazon link

You may be interested in this lecture from University College London on Sexual Orientation in the Middle Ages.

In a nutshell, the concept of homosexuality or heterosexuality as an identity and continuous mode of sexual engagement and attraction is a modern concept, and not one that is directly transferrable to other eras that had different cultural contexts.

Here's a pretty good write up on this topic, but you'll find some more that may interest you on the FAQ section of the sidebar.