Rankings of the historic universities in Europe
First: Rankings are just rankings and are, to a large degree, arbitrary. (Shameless plug: Here is an article (arxiv version here) that shows that for some specific database many players can get to the top rank just by fiddling around with some weights.)

Second: Just as some universities gain reputation, other lose some. That's pretty normal, isn't it?

Last, some trivia: You are probably even more surprised that some universities of some fame in the old days do not even exist anymore. Stupid example: Gauß got his PhD from the University of Helmstedt, a town that has nowaday less inhabitants than some German universities have students… Another example I know of is the University of Rinteln. However, it is hard to judge the standing of these universities at that times. Alas, university rankings did not exist some 300 years ago…