Is "flops" a reliable measure of deciding computational capacity?
Much computing is shuffling data around, from memory to CPU(s) and viceversa, from disk to memory, and so on. Performance could well be determined by non-processing needs. If there are several CPUs involved (many supercomputers really do the computing on graphics cards, which are massively parallel SIMD computers), jobs that can't be sped up by processing separate data streams with the same instructions will go much slower than extensively studied and paralellized to death computations like massive matrix operations.

So the answer is no, raw FLOPS aren't a good measure of performance. Again, the only reliable performance measure for your specific problem is the performance on it. "Performance" isn't a number, it is a vector with multiple independent aspects, and the requirements of your problem are also a vector, in the same dimensions. How well they match over a wide range of possible problems to a particular machine can't be reduced to a single number.