You're probably overanalysing. Sure, flags of the different parts of the UK are popular with separatists (though English nationalists, unlike Scottish or Welsh ones, tend not to be particularly opposed to the Union) but they're also the "you're currently in England/Scotland/Wales", and the "you can watch the football/rugby in this pub" flags. Probably there were a few county flags or local coats of arms on tourist sites and public buildings too.

As proper flag-based protests in the UK go, it'd be difficult to beat the bizarre sight of Cornish fishing boats and villages being covered with Canadian maple leaves back in the mid 90s when Cornish fishermen backed the Canadian side of a fishing dispute...