Football clubs are responsible for the actions of their supporters in the same way that a pub or club is responsible for the behaviour of their patrons.
Pubs and clubs get fined and/or shut down all the time through there being problems with their patrons, whether this is drug use, drug dealing, fighting, or just antisocial behaviour etc.
You can't completely control peoples behaviour, but you can put things into place to try and mitigate or prevent the behaviour. In a pub or club this might be bouncers on the door, frequent checks of the toilets, controlled smoking areas i.e. sectioned off so people can't sneak in through the back door, CCTV, systems which store id that is presented at the door to try and catch people who've caused trouble else where etc.
A football club might place more stewards in sections of the ground where the rowdier fans are, perhaps installing CCTV so that they can identify trouble makers better, being proactive and tackling the situation as soon as it starts.