It's a flag usually assosciated with racist nutjobs. Doesnt have to be, granted, but the usual way of showing national pride and unity is to use the Union Jack.
Replacing the Jack with the England flag telegraphs that unity is not the goal.
Why do Wales and Scotland get to fly their flags then? Because these were countries that England oppressed and occupied. The use of their national flags do of course have racist undertones (usually aimed at the english), but it's a way of preserving their heritage under a foreign occupier and so we grant them this clemency.
England flying their flag for the same reason does not hold the same merit, unless we're literally expressing our heritage that was taken away from us... by us. We were a worldwide occupying force for a long time. Maybe we should calm down on the pride, and instead fly the Jack that promotes more unity