1) Most players considered the elven gods to be nothing more than myth. Then along comes Inquisition to prove they were, in fact, real. Just that they were not gods. Powerful, immortal, extremely knowledgeable, yes, but not gods.
If Loghain is a fool for living in a world of magic and being blind to it, so is Wynne. She doesn't believe the gryphons were ever real. When in camp, she tells you about a battle that happened long ago where Grey Wardens fought riding gryphons. As a mage, she doesn't hide her skepticism as to there being any truth at all to the existence of gryphons.
The Circle is an institution for the education of all matters magical and it also doesn't believe in many magical things: immortal mages, harmless blood magic, a way to convert a demon back into a spirit and many other practices that are normal for Morrigan, Flemeth and that were common in Arlathan. Some of these practices are even declared to be heretical. However, we have proof in the game that all those practices are not impossible. They are very much real.
2) The Grey Wardens are a foreign (they originated in the extreme north, in Anderfels), hermetic order full of secrets that appear out of the blue to make demands from politicians and rulers. The GW had already betrayed a Ferelden monarch in the past by leading a revolt (Sophia Dryden). Later on, they endangered King Maric's life and almost allowed an Orlesian mage, Remille, to threaten the world with the help of a darkspawn (the Architect in the Calling).
All Loghain knew about Wardens is that they often took actions that endangered people and were known not to be trustworthy. Genevieve asked King Maric for help to go into the Deep Roads in order to rescue Bregan. Her motive was that Bregan knew where the remaining Archdemons were and the darkspawn had captured him to know their locations, thus preempting a Blight.
Let me repeat that in case it wasn't clear enough: she used the excuse of a Blight being about to happen with a reason that hung SOLELY on her own word (how would anyone know that what she said about Bregan was true?) to demand aid from the King.
Instead, she joins the treacherous Orlesian mage Remille and a darkspawn emissary in some mad plan to contaminate all mankind with the taint and end all Blights. Turns out the plan was actually an Orlesian attempt to subjugate Thedas throught the use of magic that infected people with the taint.
And who made it possible that a mage had the necessary leverage to threaten Ferelden with this power in the first place?
Oh. My. God. The Grey Wardens. By allowing King Maric to be captured by said Orlesian mage.
Oh dear, will you look at that. Seems like Loghain was not mad at all. He was right all along. You can't trust the Grey Wardens. They don't know what they are doing. They don't think before they act. They endanger people. Like Clarel and that Magister. Using blood magic to summon a giant evil demon? What on earth were the Grey Wardens thinking? But oh, Loghain is mad. He hates the Grey Wardens because he's a short-sighted idiot.
It's nice to read the books sometimes. They explain what was missing in the games. Such as important stuff that tells you THE MAIN REASON behind a character's motivation. Information like that is what decides if he's mad or if he had, I don't know, every damn cause in the world to act the way he did.