That's because the great achievement of the biopassport has been to place limitations on doping, so that those who choose to dope do not gain as extreme an advantage as before, which means clean riders are more capable of competing than before. But it also means that you require less doping to become an unstoppable force, because people are not capable of doping to the Pantani level now.
This does not mean that we can extrapolate from that that Sky did what they did clean, however. That requires a leap of faith that I find nigh on impossible to take given some of the names involved. It is more likely that they could do it clean than had they dominated the Tour in similar fashion 5 or 10 years ago, sure. But with all the other circumstances, we have to swallow that 4 riders from the same team - one with dodgy history, one a miracle transformer, and the team with a doctor with a shady past - just happen to be that much stronger than anybody else, and it's hard to do. Take Fränk Schleck as an example. Back in the days pre-biopassport he was still pretty successful - top 10 in the 2006 Tour with his Alpe d'Huez win - and was connected to Puerto; in 2012 he was doping (positive test at the Tour) and was still made to look like a fool by Sky. Is Fränk doping less than he was in 2006? Quite probably. But this is a guy who was dodgy then, is dodgy now, and has been overtaken by a bunch of guys who he should, palmarès-wise, be trampling all over on the climbs, and if the péloton is less doped you would then expect that the effects of doping should magnify the performances, just as Riccardo Riccò and Emanuele Sella stood out in 2008. Fränk Schleck is the same age, roughly, as Wiggins, and younger than Mick Rogers, and coming off the podium of the previous year's race. Seeing him dropped by these guys, clean, when he's doping, is tough to swallow, unless you really don't rate Fränk Schleck (and I personally think he has been overrated a lot at times) or you really have a high estimate of what the Sky quartet are capable of.