Football fans, along with all other passengers, are welcome if they a. have a valid ticket for their journey and b. behave in a manner that does not cause disturbance, discomfort, or concern to other fare-paying passengers.
Unfortunately, a large number of football fans don't purchase the correct ticket for their journey, but the cheapest combination of Advance / split / group tickets that will get them through a barrier, and rely on an intimidating group presence when any ticket irregularities are pointed out to them.
Their behaviour and general manner is also very disruptive and frightening to a lot of passengers. Excuses for it are no better than trying to excuse the riots that have happened, and the behaviour is based on the same attitude - no awareness of responsibilities, and an expectation that their behaviour will have no consequences.
I work trains on Saturdays throughout the year, and the Saturday evening trains during the football season (or weekday evening trains when there has been football on in London) can be indescribable. They are a totally different beast in the off season.
If that is an inconvenient truth, well I don't apologise for it. If stating it makes anybody feel unwelcome, well, I refer them to the first sentence of this post, and to summarise it, if they can behave, they are welcome, if they can't, they can sod off and walk as far as I am concerned. Other passengers have a right to travel in peace, and I have a right to do my job without threats or violence being directed at me.