That's a nasty URL.
Don't bother with English language wikipedia on this one; what little there is to be found in other articles is a tad misleading. This would appear to be the relevant sentence, after wading through the whereases:
"by separating the management of railway operation and infrastructure from the provision of railway transport services, separation of accounts being compulsory and organizational or institutional separation being optional,"
Essentially, if you want to run your French train over Portuguese rail, they can't charge you for their trains, only for the use of their rail. But your French train can't attempt to supply commuter rail services for Berlin, say:
"Member States may exclude from the scope of this Directive railway undertakings whose activity is limited to the provision of solely urban, suburban or regional services."
Altho apparently if Germany wanted to let you, they could.
This bit is daunting; is that mandatory privatization or act like privatized?
"Railway undertakings shall be managed according to the principles which apply to commercial companies; this shall also apply to their public services obligations imposed by the State and to public services contracts which they conclude with the competent authorities of the Member State."
I think Article 6 and 7 amount to saying that Member States _can_ finance railway infrastructure. I don't think there is any prohibition on subsidies to the organizations running the trains, but they aren't supposed to cross-subsidize. But I'm prepared to allow for my having totally misunderstood something. Ending with a bunch of stuff about what can go into a user fee calculation, and how to complain if you think you got jacked around.
This is fairly amazing stuff. Clearly someone sat down, realized the problems associated with having any entity control track and trains, the desirability of running trains on each others track, and that if you try to solve this by privatizing absolutely everything, you'll get conglomerate/rollup/M&A crap abusing whoever is responsible for track maintenance and said, screw it, let's just separate and regulate. Of course it could in theory be solved by having One Railway To Rule Them All, but that seems pretty unlikely. Even in the EU.