Will it be too much for them?  It depends on a whole lot of things.

In general I would say go for it.  It’s a great way to see Europe.  With kids those ages make sure to check out the various benefits that different train companies provide.  They can travel for free on many routes (depending on the age, the country, the operator, etc . . .) so before shelling out for tickets do your research.

I would suggest picking a few base cities or towns and staying there for a couple of days at a time rather than maximising the time on trains and the number of places visited.  Kids will get pretty tired of getting up early, rushing to the station, getting on a train, getting off a couple of hours later, finding the accommodation and only having a few hours before doing it all over again to a new town.  Base yourself in one place for a couple of days, stash the luggage and take day trips if you want to see other places nearby.