Sympathize? He says he understands the templars. To me it seems he can understand why they are feared in the Chantry territories - mages lobbing fireballs in broad daylight, not surprising muggles would fear that.
For mages, the Chantry means a life sentence without parole (at best) or being abused by drug-addicted nutjobs like Ser Alrik (at worst). Were I a mage in Thedas, I'd take Tevinter any day instead of that.
Being sympathetically aware of the character or nature of something is, in fact, a proper use of the word "understand". I may have read into that more than was appropriate, based on the context that a fairly jarring experience was also mentioned near the use of the word understand, but that doesn't mean your interpretation of his letter is the only valid interpretation.
The fact that Feynriel is incredibly special goes a long way to help him fit into Tevinter life, and you can't expect every other mage to fit in as well. Even if we take Feynriel's letter as unadulterated praise of Tevinter, many mages have to traverse many miles of hostile territory to get there, for a less than guarantee, and in addition some mages might be wholly opposed to the use of blood magic or slavery the way Anders is. If they are absolutely opposed to slavery, and this informs their rebellion against the Chantry, they might see Tevinter as no better than the Templars. This is probably doubly true if they have believed any of the Chantry propaganda about Tevinter at some point in their life.