Some oppose the chantry because they oppose organized religion. Just as some defend it for the same.
It is no more moral or corrupt then anything else in Thedas, it just happens to be one of the more powerful.
The Chantry has good and bad
The Dalish have good and bad
The Templars have good and bad
The Mages have good and bad
Ferelden has good and bad nobles
The imperium has good and bad Magisters
The imperial chantry has good and bad
The Qunari have good and bad
The dwarves have good and bad
Examples of bad: Dalish Clan in ME, things we learned about elves of Arlathan in ME, templars being portrayed as Thedas Nazis in DA2, Blood mages/abominations/etc, Howe, the King who attacked and banned the grey wardens, Magisters in general
. lack of personal freedoms in the Qun, the Carta, Dirt Town, Classless, surface dwarf hypocrisy, killing one of their own cities to keep their economic connections with the magisters running smoothly, etc etc etc
The issue is that the Chantry has had a very prominent role in most of the games, and was largely portrayed horribly in DA2 especially compared to the amount of exposure we have actually had to the evils and negatives of other races, organizations, and countries.