Yes, there are many considerations, but if yours is just price, you'd like to see a search engine that looks for the cheapest way to get between cities regardless of whether you do it in a plane or train, right?
Well, there's one that does that. It's Danish (but don't worry--the site is in English). Momondo searches both airlines and rail connections between cities you enter, and returns fares sorted by price. Nice.
Is Momondo perfect? No, but it seems to do the best it can. For example, if you search for fares between Milan and Rome Italy, you'll find lots of airline fares but only one train fare--for the more expensive Eurostar Italia trains. You can get between those cities cheaper by using slower trains, but the problem is that Trenitalia doesn't sell those tickets online. Momondo can't find what's not online, so just keep that in mind as you give this new price comparison engine a spin.
You'll find some interesting comparisons between train and airline fares for shorter routes like Paris to Lyon, where trains are more likely to be less expensive and far more convenient.
Try Momondo. If anything, it's a good idea that will likely help you sort though your transportation options in Europe.