I mean, what are you looking to go to? You need to be slightly more specific.
Bus might be cheaper, but the train is your most common way of getting from big town to big town. If you're in England, you can get anywhere with a train ticket. Heck, if you're going across Europe, they do have EuroRail Passes(prices have gone up a bit) where you can basically travel wherever for a flat fee. You pay up front, then schedule your trips, and go wherever. That said, it's cheaper if you just do individual if you're only doing a couple of routes/stops. If you're going to do all of Europe (or at least 7-8 countries) a EuroRail pass could be a better option. If you're just doing like France and Spain, or England and Scotland, I wouldn't get a EuroRail Pass.
Airfare is also way cheaper than you think. I would highly, highly recommend you sign up for the email for Scott's Flights (don't pay premium unless you're expecting to take a number of trips). While you can find some of the deals on your own, the service emails out cheaper tickets they find, and if you're not completely set on a day, it helps you get a good deal.
As for going to matches, my recommendation would be to find the major fan forums for clubs you're looking to go to. They're pretty helpful. BigSoccer forums were pretty helpful in what to do when I went to Liverpool. If you're trying to go see matches for major clubs, you could also contact some of the supporter groups and see what they have as far as info. As has been said, the club websites are also a resource. They're more than happy to have you, because they know you'll probably take a tour and buy some stuff.
Really, big matches are the main ones that are difficult to get to. You're not going to United / Liverpool unless you know someone or pay a big price for 3rd party tickets (which can be dicey in many countries, with fakes, scam sites and overselling relatively common). Some stadiums sell out, but if you look for matches in League Cups, you can often find affordable tickets, even day of. You do want to make sure you're wearing some either nondescript clothing, or make it clear at the box office you're a tourist. My sister got to go to Stamford Bridge, Craven Cottage, and White Hart Lane with cheap tickets to see matches when she was there on a winter semester for cheap. She just went day of, said she was a student, paid the price, and sat with the other tourists/out of town people. They didn't see any particularly great matches, but if you want to go, it's not crazy hard. I mean, you can go to basically most of the Bundesliga or Serie A matches without much trouble if you want. The only thing you're going to struggle to get is for some of the bigger matches for massive clubs, or the derbies. Sure, they're not cheap, and many places are going to try and gouge out of town visitors, but it's doable.
I would also say that don't completely rule out some of the cities until you have a plan. While I wouldn't want to spend a number of days in Liverpool, if you can time it to do a match there, and a match in Manchester, it's worth doing that. There's enough touristy stuff in Liverpool (Beatles, Liverpool One) for a day or two, but not much more. If you're getting the most bang for your buck, and want to do cultural stuff, then you need to stick with the major touristy hubs. But understand that it might also limit some of your football match options if there's major tourist areas. Some of the bigger cities do also have access passes. It was a bit of a weird experience for me to travel overseas a number of times because you have to pay to see everything. Living close to DC, we don't pay for basically any museum. They're all free. In Europe, that's really not the case at all. So, like London, Paris and the like have passes where you can get into everything for flat rates. But you better be ready to hustle. They're not worth it if you're going to do one or two things and then hit up the pubs. They're only worth it if you're going to bust your backside to get to stuff.