I've thought about this for a while and I think the "fast prototyping" reputation is an accidental feature that sticks because of history.
Python and Ruby were just better languages than Java 1.4, C++, Perl and PHP were at the time. They were so much better for not only prototyping, but writing - it was easier to get something working and iterate in Python than it was in Java. And not only were they better, they were better at the right time when the internet exploded.
Now, it largely feels like languages like Java and newer languages like Go have caught up, but Python and friends still enjoy the feature of "fast prototyping." Now I think this is because since they had gotten so popular, they now have a massive ecosystem of libraries and idioms that makes it so easy build applications.