Yes, but what he said was true, they were not tolerant. Bioware can create the world they want, that's fine I don't mind, but still if medieval fantasy in a realistic sense is their aim, bigotry, hate, and senseless violence need to be included. But perhaps they don't want a realistic medieval feel.
One key thing about medieval European society was the Pope. Namely, that the Pope was male, the kings were male, a lot of kingdoms had male-only succession laws, the priesthood was male, the warriors were male...Basically everyone in a position of power and prestige, with a few impressive exceptions, were male.
In Thedas, their version of Muhammed/Joan of Arc/Jesus was a woman. And the Chantry, the bedrock of society, decided that women would be the only ones who could achieve higher rank in the Chantry. The Divine is female (In the South, at least.
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I think that Andraste and the set-up of the most successful Andrastian religion is responsible for women having a lot more power and rights in Thedas than they did in our own society. 
As for homosexuality, unlike some others, Andrastianism doesn't seem to have had any tenets or preaching against homosexuals. Just mages and Tevinters. 
And the Tevinter Imperium's views on homosexuality mirror that of the Romans, at times.
Instead, we've got: anti-elf bigotry, the various prejudices amongst the elves against each other, Orlais being hated by everyone, the Orlesians looking down on the Fereldans as primitive yokels, the various split-off groups of the Alamarri's hatreds for one another, Hawke and company being spat on as refugees as they try to make a life in Kirkwall, mages being oppressed, Templars being addicted to lyrium, the Chantry often acting as an arm of the Orlesian Empire, the Qunari with their religious fanaticism, the mass slavery of Tevinter, the mass poverty and abuse of elves and the poor in the South, peasants stirring up revolutionary talk in Serault, the Casteless in Orzammar, the Orlesians' tendency for mass arson, rape, and dog-kicking whenever they occupy a country, darkspawn raids, and blood magic libel.
There's plenty of unpleasantness in Thedas. It's just that Inquisition focused less on that than some of us would have liked. I would have loved to have seen more of the Briala-led rebellion, the brutal Chevalier oppression, Avvar raiding the Hinterlands, that kind of thing. I hope that the DLC gives us a view of Thedas's darker side, as Bioware handled some pretty heavy and dark plots with finesse in the past.