Not because the theory behind them is flawed, but because there is no practical way to mass produce them. One of the key's to the explosion of semiconductor based devices is the ease with which they can be constructed. There are also other problems that will pop up even before the transistor size one. Other people here disagree with me though. Here is a thread I started here not to long ago on a similar topic.
Life is complex.
It has real and imaginary parts. Even quantum computers will be using the idea of transisters. But, instead of transistors made out of semiconducting material, they will be made out of Atom strings like proteins or nucleac acids. It's still the same idea, though. They will simply come in new forms.