I think it is unfortunate (and showing more than just a bit of ignorance) when individuals or groups feel it appropriate to deface their national flag with commercial messages or political slogans. But, like Jock Scot has said, it's nothing to get too wound up about.

The sad thing is, at least in Scotland, a group like the Society of William Wallace could, in theory, apply to the Court of the Lord Lyon for a grant of arms and display those instead of defacing their national flag.