To be fair, they may not consider themselves English over British. I don’t know how they define themselves. Why do they have to choose?
If an organisation, or someone speaking on the behalf of one, expressing a preference or giving special treatment to just one member of a group, rather than staying neutral or supporting all, it is going to cause resentment, and a feeling of detachment in the rest of the group. And this is amplified when it's happening across the board. In tabloids, on TV, by government officials, by supermarkets and brands.
You could say this only happens because England's the most successful team. But this is happening all the time, even when Scotland and Wales are active in competitions. It happens in British wide weather reports, in supermarkets in Scotland, with "congratulations to England, from Tescos" and England flag bunting, and England players posters in the windows and such. I've never seen that for Scotland, in England. Nor would I expect to see it.
And like I said, it really just lifts up the British mask to show how to establishment really sees things.
It's systemic. Like "Britain's" Got Talent only reviewing contestants from across England, for the first several years, and only including Scotland when they were called out on it.
"I don’t know their origins, but why not? Just as Scottish companies are proudly Scottish but don’t restrict their trading to north of Newcastle. "
If they're explicitly British companies, as mentioned above, but only backing one national team, they're expressing a preference.
If they're Scottish, Welsh or English, that's fine. But then they shouldn't present themselves as a British brand, only to act as a Scottish/English/Welsh one when it suits them. Especially when it's only done for one, rather than for all of them.
If Tesco claims to be British, but only goes all out for England, and none of the other teams, then don't complain when people call it out as English, and feel disconnected from it.
A lot of this could be resolved, but there doesn't seem to be an appetite to do so.
I don't begrudge English fans getting behind their team, at all, Just the English defaultism by British media, gov't, and companies.
Maybe it's something that you are only really aware of, when you're not English, whilst subject to British media and British companies, claiming to represent all of us.