Steve Jobs is already facing pressure over allegations that Apple charged a different price for songs depending on where they were bought. Back in 2005 a song from iTunes cost €0.99 (or $1.38) in France and Germany while the same song cost £0.79 (or $1.59) in the UK.
But this issue isn't the main issue for the EU. What the Commission lawyers really want to get tangled up in the the iPod/iTunes ecosystem that Apple has created. Just in the same way that the Commission objected to how Microsoft forced Windows Media Player onto Windows users, Apple has done exact;y the same with iTunes. In much the same way that the bundling of WMP froze out competition, forcing iPod users to go with iTunes does pretty much the same. Just as the Commission forced Microsoft to carve off WMP from Windows (going as far as to make Microsoft offer media player free version of Windows (a product which both consumers and OEMs alike have enthusiastically ignored), it's very likely that the iPod/iTunes ecosystem will be broken up.
After all, bundling is bundling.