One of the more obvious aspects of this is price. If you're paying £2-3 for a game you're expectations aren't too high, as opposed to paying £40+ for one. Also, the label 'indie game' automatically lowers your expectations, and any downfall can be explained by simply saying "it's an indie game, it's probably developed by one dude, back off".
I agree that Indie games are an exciting endeavour. They're not a new idea, not by a long shot, indie games have been around since the early days. But it's new platforms like the iPhone store and Steam that are really bringing this indie games into the spotlight and making them a profitable industry.
It's undeniable that the vast majority of indie games are utter shite. Seriously, browse any flash game website and you'll find that only about 25% of the games are worth any merit. The same goes for the Xbox Live Indie section. As this video elaborates;
The video is only really highlighting the bad games, but it made me laugh quite a bit and it goes to show that indie games aren't all like Minecraft.