Comment by jltsiren
Basic text formats persist, because everyone supports them. Many tools have better file formats for internal purposes, but they are rarely flexible enough and robust enough for wider use. There are occasional proposals for better general purpose formats, but the people proposing them rarely agree which of the competing proposals should be adopted. And even if they manage to agree, they probably don't have the time and the money to make it actually happen.
Also for historical reasons I think, since Perl used to be the big bioinformatics language, and it is surprisingly hard to compete with in string handling.