The gist of this book seems to be that homosexual men weren't methodically persecuted, really - up until the rise of the inquisition and the witch hunts, that is. Before that, there is only very little data on everyday life, but it seems that if there were people who lived in same-sex relationships, they did so secretly.
Homosexual behaviour was forbidden, of course, but apart from the handful of accounts which do exist of trials in which anal sex and homosexual paedophilia was the primary charge in Europe, people engaging in homosexual behaviour seem to have led a rather undetected life. The other trials which do mention homosexuality seem to do so only on the grounds of adding more charges and underlining the moral depravity of the people charged - usually with large-scale theft and/or murder.
It is noteworthy that homosexuals were referred to as "Ketzer" (heretics), and anal sex was known as "ketzern" - to go against the order of nature as god apparently intended it was heresy. When the witch hunts began and the tempers started to get tetchier the mere accusation was enough to light torches and the wooden stakes.