Because I tend to blame people for things they actually do, and not stuff speculated upon. Since Loghain is responsible for so many other crimes that we find ample evidence of in Origins, and not one scrap of anything, no codex or snippet of dialogue (even a rumor, which, at best, would be hearsay) of any alleged involvement in the Cousland massacre, I am going to give him the benefit of the doubt on this one. All I've ever seen as proof from those who include him in some JFK-like conspiracy theory is speculation upon more speculation about the nature and motives of Loghain and Howe.
We discover notes in Awakening that discuss Howe's plans for the Couslands with other individuals, but nothing that ties Loghain to the massacre. Nothing that even mentions him. We can even sit in judgement over some of those who were supporters of Howe, and no mention is made of Loghain.
At most Loghain didn't do anything to Howe when he learned what he'd done, but by then Highever was in Howe's hands and Loghain needed him.
And this is from someone who doesn't like Loghain, and has killed him in all but 1 of a couple dozen playthroughs.