TPM didn't cost 100 million to convert. How could any movie make money in 3D if it cost an additional 100 million? Next to that figure it is relatively cheap, which is why so many films do it.
The 3D conversion of Episode I, based on my own experiences and research in 3D conversion, cost about $15 million or so. The film made healthy profit, just not nearly as much as what they expected. Much like the 2008 Clone War film. By most standards, and x10 by SW standards, it was a bomb. But it wasn't. It was a cash cow. Hell, the Holiday Special was probably fairly lucrative. But yeah, I agree it was a bomb, in the sense that it was a huge disappointment. But at the same time, it came out in the black financially (as far as I can tell, but not by much mind you). I guess it depends on what your criteria is.