Radiowaves or any form of electromagnetic radiation have no medium through which they propagate. Michelson and Morley in 1887 proved experimentally there is no "ether". Maxwell's equations (the equations of electrodynamics) show that there should be electromagnetic waves in free space. You can show this in two minutes of calculation. Not sure what you mean by "they were closer to the truth the first time." Physicists for over a hundred years have thrown out the possibility of "ether" simply because empirically it doesn't exist.
http://en.wikipedia.org/wiki/Michelson-Morley_experiment
We don't refer to Descartes' doubt everything except "I think therefore I am" philosophy when trying to understand natural phenomena. There are other philosophers, many who do not subscribe Descartes' philosophy, does this have any bearing on the explanation of radio waves? Uhm, no.
If you are a scientist, then you do believe that theories can be proven true not just dis-proven, or why would anyone bother to devote their lives to coming up with theories. This is actually a very important and interesting philosophical question (philosophers would call this the philosophy of science) and you are referring to the old philosophy of science called demarcation due to Karl Popper. My point is what constitutes a truly true theory is an a very open question.. people have been arguing over it for quite awhile and will continue to do so.
A philosopher can't answer the question of say if you take a car and start stripping parts off and replacing them with the same parts but physically different ones at some point you would say this is a different car even though it looks the same, drives the same, you still have a sense that the car is a different one. Say you replaced all the parts.. it would have to be a different car. If you only change one screw, you have the sense that it's the same car. At what point does it become a "different" car?
In light of all of that, like I said physicists know with 100% certainty there is no such thing as "ether". Ether being the medium of electromagnetic waves in the same sense that water or fluid would be the medium of waves on the sea. We did the experiment in 1887, we can do it today, in fact I'm sure there are modern and more accurate versions of this experiment and at no time did any physicist say oh wait maybe we were right..
Anyhow, lecture over...