I'm unaware of any specific evidence about rape statistics during the Middle Ages, assuming you're limited to Europe. Thus its impossible to scientifically gauge how much rape there was then compared to any other time. Even rape as a result of war is not detailed in any clear way. For all we know there was less rape then. You could speculate, but it would more in the nature of a sociology/psychology answer.
The problem is that records from that era were not all inclusive of everything that occurred. Often accounts were written to achieve a goal rather than as a matter of data collation. The policing of crimes was haphazard and poorly documents. The bureaucracy of state was a fraction of what it is today. Power differentials between individuals were far more all encompassing than now and personal liberties were not as clearly articulated as they are today. Thus if a Duke has his way with a serving maid, was that rape? Did she acquiesce out of loyalty, resignation to her position, the hope that a pregnancy would result in royal bastard or just because she fancied a bit of nookie. Rape within marriage didnt exist as a concept, for either side, so was marital forced sex rape or not?
Rape certainly occurred in law, but there are no stats about numbers. Perhaps in future you could narrow it down a bit or provide evidence that what you propose is even true.
/u/Thecna2 hits the nail on the head by identifying a difference in attitudes towards what constituted rape or assault in the Middle Ages.