It was a fad in the early history of motion pictures and it's still here so I think its a fad that's here to stay. The difference now is that with digital implementation, it can be done much better but I think it has a ways to mature for the home theater market.
There are several things holding it back including cost and lack of media (movies on BD), lack of standardization between systems used by manufactures (types of shutter glasses, etc.), and lack of 3D home theater equipment (lots of 3D "Ready" projectors, but no solid 3D home theater system yet (I'm not referring to flat screen televisions here, which are of course plenty).
It's interesting to note that there were far fewer 3D televisions and displays this Christmas in stores (at least in my area), than there were last year. I think 3D has received a lot of negative publicity and its a real mish-mash of offerings right now. Some televisions require adapters, some are now passive, and it goes on and on. I do think the move to passive glasses as LG is doing, will help some of the issues.
When more movies are available for reasonable prices on BD, and some a bit more technical evolution takes place, 3D will become mainstream, but it will be secondary to 2D content for some time.