The problem with the "Circle towers protect mages from mobs" argument.

It is probably true that mages may have been set upon by mobs in the past but the question would be, why? Is it simply because the Chantry have impressed upon them how dangerous mages are or did that particular mage do something to antagonise them?

Now so far as DA2 is concerned, clearly the refugees from Ferelden can spot the difference. They are actively protecting Anders from the Templars because they realise how much they benefit from having him around to treat them for free. This is the odd part about protecting the mages from the people claim. Once a mage has been trained to control their powers, what would be the harm in letting them out to use their magic beneficially? This even seemed to be the case in Drakon's time before the Circles were established and may be even after, since his family were from Tevinter and so he would be familiar with the concept of having mages being properly trained.

World of Thedas certainly seems to suggest that was the case, except it states on p.95 that mages were permitted to serve the ruling class provided they did not use blood magic and did not unduly influence them or become rulers in their own right. I assume that is how the Mortalitasi were able to become established in Nevarran society since this was well after the Chantry was established in the south but before the discovery of the extent to which mages had resumed control of Tevinter. However, you will notice how they were only permitted to serve the nobility, not the ordinary populace. So overtime, the sight of a mage became less familiar among the ordinary people and the teaching of the Chantry reinforced the idea that they should fear them. As was evident in DA2, the mage children of nobility are treated differently from those of the peasantry and that is likely why the ruling class were happy to back these strictures.

So when a mage child is discovered among the ordinary people, they immediately report them to the nearest Templar to get them taken away. Occasionally, a family will conceal them, which can go horribly wrong, as happened with Meredith's family. However, I think for the most part that the ordinary villagers would be too frightened of the mage, even as a child, to actually attack them but might well shun them until the Templars turned up. So, the child would sense their fear and if subsequently told they were being taken away to protect them from the mob, they might well believe it.

Essentially, as you say, it is propaganda rather than reality that created this idea of "protecting the mage" from the people. There would also seem to be a element of self-fulfilling prophesy when it comes to "protecting the people" from the mage, since it would seem many young mages are so unhappy in the Circles and so fearful of their own powers or being made tranquil, that they end up self immolating or becoming possessed.

Mind you, that said, I seem to recall that the real Cole had to hide from his father who wanted to kill him for being a mage and then I think killed his father before the Templars found him and took him to the White Spire. So I suppose enough instances like this could occur that the Templars can point to real anecdotes to reinforce the idea that the mage needs protecting from the outside world.