I wouldn't look too much into it. It's obvious that if Lyon make it, they'll get one of the hardest draws next round, either Marseille/Inter or Zenit/Benfica. Regardless, I'm going to enjoy when they finally get a big gun and get trounced whether it's the semi final or quarter final. I'm not one on conspiracies mind you, but the Lyon fiasco and Platini being French and generally looks like a douche, make me a skeptic for this scenario.
Lyon are a very talented team and aren't getting any credit because they don't play in England, Italy, or Spain. I think there are very few teams left that would "trounce" them. Barca or Real would but not much else.
Well, let's have a look at Lyons luck in recent 2nd round draws: 2008 Manchester United 2009 FC Barcelona 2010 Real Madrid 2011 Real Madrid 2012 APOEL Yup, it's unbelievable. They always get the most attractive clubs out there, clearly they are cheating... though obviously, someone slipped up this time around, who would want to play lowly APOEL.
So, you would have suspected APOELs opponent of cheating no matter whoever it was? ManU, Barca and twice Real is quite tough even by CL group winner standards. APOEL is ridiculously easy by the same standard, but someone had to draw them. And I think it's nice that Lyon got someone easier after the last couple of years. I do admit that the last CL matchday looked fishy (more because of Ajax' 2 wrongly disallowed goals than Lyons high win), but that's a different story.