The Chantry teaches us that magic is to be used to aid man but never rule him, and after the reign of the Tevinter Imperium that philosophy stands more true than ever. The Templar Order is tasked with corralling mages into Circles of Magi where they can be watched with a careful eye. Some view this as beneficial, a precautionary measure that is for the safety of everyone including the mages themselves. Some believe this to be cruel, unjust subjugation.
As with most things, it's likely somewhere in the middle...