With flag burning I feel like there's always some level of self criticism there, it's say 'I'm so disgusted with my country that this is what I'm doing' but at least you're owning the thing you're being angry at and want to change.
Burning someone else's holy book feels more like an attack on another culture, blaming something external for all your problems, I think that for some people there wouldn't be a big leap between burning the book and burning the people who wrote it.
As has been said, most defenses of flag burners are about whether or not it should be illegal, which is only even an issue because the fringe people on the other side of politics like to bang on about how it should be illegal. It would be interesting to know where this group stand on it.
I don't see a contradiction between thinking flag burning should be legal and Quran burning is offensive. Hell, they can both be legal AND offensive. Though the words I'd prefer to use are hateful, petulant and downright childish. Seriously, 3000 people die, a nation comes together and less than 10 years later the best publicised memorial is a group of small town bigots using it as an excuse to hate on brown people, poor show.