It's very simple. I have nothing against Moncoutie. I hope I am wrong and he is clean.
The problem is he wins big mountain stages against prominent climbers from prominent doping teams. Yes, many of these stages are wins via break, but riding in a break and defeating excellent pro riders also takes stamina and power, which are greatly enhanced by PEDs. The whistle blowers have indicated it is not possible to win Vuetla stages clean, and I give more credence to them than anyone else.
Generally, I don't think it's possible for clean riders to win any significant professional race, and that's mostly because oxygen-vector drugs convey a decisive advantage. It's the same in any sport where endurance and power are factors.