When a plugin is updated, its folder gets deleted and recreated with the updated version. This would destroy any caches, which on a heavily trafficked site could bring down the server
Additionally, the plugins folder on a lot of servers is read only to the user the web server runs as for security reasons.
It also improves management. If you want to clear cache, you don't have to empty multiple folders across a site, when you have a single cache folder to clear out.
But keep in mind though, that all these plugins give tiny improvements when compared to the massive boost a dedicated object cache will provide. I strongly recommend a Memcached/Redis based setup.
Also, file based caches won't work on a lot of systems, e.g. on a busy cheap/shared host server, it might be faster to generate the page than it is to retrieve it from the disk, with the end result being that your site runs slower not faster