Kvetching can be useful for relieving one's stress ;-)

Leaving out the comparison to C++ (and kvetching about your ignoring Fortran, which is still used for numerically-intensive programming), I suspect that Java benefits from its supposed (and non-existent) perfect portability and its general similarity to C++, while Ruby has benefited from The Art of Computational Science by Piet Hut and Jun Makino. Perl certainly does suffer because of its history of use in string manipulation and system administration.

The bit about sysadmins is probably a larger factor than many scientific or engineering software developers will admit. In most of the engineering environments in which I've worked, the sysadmins have been felt to be most concerned with keeping people with domain knowledge away from the computers. Since sysadmins are viewed as obstructions, their tools are going to be deprecated.