Dear Emerson, the "weak Fourier transform" of the potential, which is simply $4\pi / q^2$, is the "proper physical" value of the Fourier transform.
In physics, it simply makes no sense to say that a Fourier transform "doesn't exist": the Coulomb potential clearly does exist, and when we're calculating something that depends on its Fourier transform, the answer also has to exist because the world has to behave in some way. It's just generally impossible in physics to say that a valid theory produces an "ill-defined answer". We must always struggle to get an actual, well-defined answer.
And quantum electrodynamics, even though it has a superficially divergent Fourier transform of the Coulomb potential, is an excellent theory. Still, we need the Fourier transform to answer many questions. So the only question can be how to find out the right answer - not whether an answer exists. Of course that it does. The physically correct answer is most easily obtained by regulating the potential - as a limit of the Yukawa potential - and by exchanging the limit with the integration in the middle of the calculation, to guarantee that the result is sensible.
This is like giving a mass to the photon - we call it an infrared regulator. Such things are omnipresent in quantum field theory. If an expression doesn't naively make sense, one tries to express it as a limit of a more general expression, and calculate a more general calculation, which is more well-defined, and try to take the required limit at the very end. This is the right physicist's approach to seemingly ill-defined expressions and it always leads us out of the trouble and it always tells us something more meaningful.
A failure - a refusal to calculate the answers - is just not acceptable in physics.