If someone goes around desecrating Torahs, you would be completely rational to conclude that he probably has an issue with Jews in general and feel threatened.

Here's a possible litmus test: how would you feel about another former Orthodox Jew desecrating a Torah scroll as a symbol of eir change in belief.

I think I'd still feel emotional unpleasantness although probably not as much as in the generic case. This suggests that Vladimir's concern is partially correct but that that's not the whole thing and some really is just residual emotional feelings. There's another side issue that may also be involved, in that the burning of books of any form or similar objects (such as scrolls) makes me deeply pained regardless. But that connects to what Vladimir M was talking about in that part of that deep pain is the historical connection between book burning and censorship.