Simply put...some people don't know any better. I was at a bioinformatics presentation yesterday where the term "using Java instead of some crap Perl" came up. I wanted to tell the guy "yes, you can write crap in all languages", but few understand this. Why? I don't know. I write quality code in all languages -- except languages I'm not familiar with. My guess is many folks have seen the work of inexperienced Perl coders who lacked a little discipline or training, since Perl tends to have a lower barrier to entry (but a much higher barrier to mastery!) as compared with something like C++.
The worst Perl stereotype I see is that "Perl is line noise" or "all Perl code is unmaintainable", but this is clearly just that -- look at all the great work here, a lot of extremely brilliant folks, and the coding (at least to me) seems more in line with the annals of Lisp (and other A.I. languages) and more esoteric OO (not-confined by the limits of Java), making Perl feel like a great choice for academic-type coding.
I think the only way to fight this is education. I'm not a language bigot, but I do find myself hating languages that are full of them, hence my crusade against using Java everywhere -- especially where it is not the best choice. Like in that presentation where an XML-based system was being used, but the middleware was exclusively java. Why? No need -- it should support many tools.
I like folks that keep an open mind. Just learn a bit from your TA, but don't believe him when Perl is just for text processing. Text processing is less than 1/8th of what I do with Perl.