If they want to target muslim extremists they could burn a Daesh flag. But they burn the Quran because they don't want to target the extremists. They want to target all muslims, which is why they choose the symbol of all muslims.

In the same wake you wouldn't burn an EU flag to criticise the hungarian government. It would of course be understood as an attack on the EU and all EU countries, because you know, you could just take a Fidesz flag. (Arbitrary example, the same would work for any country, political party or figure)