The reasoning behind the brown bottle is that the colour stops ultraviolet light from penetrating the glass. Ultraviolet reacts with the hops in the beer which results in a skunky smell and/or taste. The hoppier the beer, the quicker the reaction.
Ultraviolet has no problem penetrating green and clear bottles. If you want to buy beer in green or clear bottles, look for ones in boxes or reach far in the back of the shelf where there is less light. Fluorescents also cause this issue.
And yes, it is unfortunate that Pilsner Urquell comes in green bottles. This has got to be the biggest bonehead move they could have ever done.