The protection offered by Ferelden which resulted in the mass chaos of the Hinterlands that's dwindling their numbers?
The protection offered by Ferelden which allowed Fiona's mages to live in relative safety of a castled town while mage supremacist breakways had choas away in the countryside, yes. This is what castles protect you from, after all- the dangers outside the gates.
To criticize Ferelden's protection as insufficient would likewise need for Alexius's protection to be more sufficient in comparison. What protection did Alexius provide against the same mass chaos of the Hinterlands that Teagon could not?
And again, all the recrimination about "you made your own bed" is beside the point when we're discussing what she should have done next. I'm not disagreeing she made bad choices and was a bad general. I didn't like her in Asunder, or Adrian, though if the Conclave had yielded fruit then the mage rebellion would have looked much better in retrospect.
What she should have not have done next was to tie herself to an unwinnable backer at the expense of a friendly backer who would certainly retaliate. In inviting Alexius in and tolerating his coup of Redcliffe (and then not leaving to the east with Teagon), Fiona tied herself and her mages into a stationary location that was inevitably going to be put under seige.
And was, three times, and only resisted falling thanks to an unchecked Corypheus. If siding with Corypheus can not be used against her, she can not claim the security derived from it.
Ferelden's protection may not have been sufficient, but it was there and the threat of a Templar siege was more hypothetical than realistic. Alexius's protection was not going to be sufficient, in large part because the threat of a Ferelden siege was a guarantee after the mages stood by and let the coup occur.
They're right that the Chantry was never going to voluntarily relinquish control over the most valuable human and natural resources in Thedas.
Considering that the Chantry never controlled their labors or forced them to work as natural resources in the first place, and was open to negotiations and compromises to loosening their control, this is just wrong.
The fact that Fiona explicitly sold herself and hundreds of others into involuntary servitude as resources makes the objection more than a tad hypocritical.