(Off topic I know, but there is plenty in our history and the current attitudes of the government and our population towards certain groups which prove why we are not a great country and why some might feel ashamed of our flag, and prefer not to have it plastered over everything. Some of those attitudes are even on display in this thread!)
The issue isn't the flag, which I am sure everyone is proud of (even non-nationals are likely proud of it if they've chosen to live here), rather the issue is the people that choose to use the flag as a political statement to show some sort of superiority and use their freedom to fly it as a way of attacking foreigners. The people who say 'If you don't like it, why don't you leave' that you'll find anywhere you look - newspaper letters pages, social media, forums, news site commenting sections etc.
The flag got hijacked by the nationalists, and many people who are proud to be British won't fly the flag to avoid being associated with them.
That's the problem. People become scared to fly the flag, and those who demand we protect the flag are the very people that stop others from doing so.
The solution would be to 'reclaim' the flag. I bet if some communities proudly flew the flag in their front garden, we'd see a lot of people suddenly lose interest.
There's nothing to suggest GBR will see the Union Flag draped across our trains, or booking halls having flags hanging from the ceiling. It's just that the launch was very much portrayed as 'getting our country back' by a Government desperate to get some wins.
It is worth noting this wasn't really mentioned or considered by the press or the public interviewed. That's because it's a train service and people care about trains running on time and not costing a fortune. Absolutely nothing else matters to them, not the name, the colour scheme or the typeface.