Woah, wait a second, dude. (EDIT: Sorry, Rebbecca. Sister.) 12 cities in 15 days? That's one itinerary that needs a little changin'. I'd say right in half. Or extend it to 30 days.
Possible in 15 days (and this is at a brisk jaunt, no time for lollygagging): London, Brussles + Bruge, Berlin, Prague, Budapest, Vienna, Salzburg (which IMHO you can skip or just stop here for coffee), Munich, fly back to London and byebye
15 days (again, jaunting) London - Paris - Nice - Florence - Rome - Venice - fly back to London and byebye
You can get cheap one-way tickets from a discount air carrier like Ryanair for the hauls from Munich or Venice back to London.
The bus is cheap, yes, but is not nearly as flexible as you need if you have to get so much done in so little time. It also is a b*tch to sleep in - in the train you can stretch your legs out a little bit at least.
Otherwise, you are right, there are some additional fees the train services squeeze out of you for "improved services" (travelling by Intercity train, for example) - those go for about twelve to 24 bucks a pop. The train in the Czech Republic is not covered by Eurail, true, but the prices are not formidable - about ten dollars for the Berlin-Prague route (you only pay the section from the Czech-German border to Prague) or a little over 20 for the Prague-Vienna stretch (again, only from Prague to the border), plus those surcharges ... well, yeah, it does sort of add up, huh.
In the Czech Republic and Hungary, travel times by train and bus are about the same. In the other countries you mention, though, the trains are MUCH, much faster. Plus the connections run more often.
So you need to think if the restricted timetables, restricted movement within the bus, slower travel times and endless views of highways are worth saving 400 bucks. If you only have 15 days, you may just need that cash for the next time you come back ... because there is no way you can do all those cities by bus, and you'd be hard pressed to do them by train, unless you plan on just being in the train (almost) the whole time.
The only cheaper way I know of travelling in Europe is through Mitfahrzentrale, a sort of organised hitchhiking system. But you have to be incredibly flexible in terms of time, definitely not in a rush. It would make sense if you were on the three month (or longer) plan.
So there you go, less time = pay more.
Came for four days, stayed for 18 years (and counting)