The Union Jack is a symbol of empire and colonialism which the St. George's Cross isn't.
However, the football thing is more recent. If you watch "the Italian Job" from the 1960s, the England fans wave around Union Jacks instead of their own specific flag (as Scotland and Wales fans would). Clearly in the intervening years, England fans have discovered the England flag.
Scottish and Welsh people seem to be a lot more comfortable with their identity than English do. And that includes their flags. I have seen countless bits of research which suggest that ethnic minorities happily identify as Scottish and Welsh in Scotland and Wales, but in England, they identify as British rather than English. I suggest you read Billy Bragg's "the Progressive Patriot". He is an English socialist who has tried to reclaim English identity from the far right, which he is entitled to.