It makes a lot more sense when you consider the history of it all, but the admins have made this a general purpose instance it really has little to do with it anymore.
Because the main instance is a drop in the ocean that the lemmyverse should be, so it makes sense to call it a "millilitre" (ml). [inb4 I'm making shit up.]
it could be a result of a trend for non profit social networks to use .ml
ml is a less used domain. so it could be a cost saving measure as .ml is a completly free, low barrier to entry top level domain. (TLD) - the Malinian government gives away the domains for free, with restrictions. and you can essentially remove most restrictions by paying a small fee, so its a very low to no cost solution.
quite often - .net, .org, .com all have restrictions over who can buy a domain, and what for. As they are more "premium" top level domains.
I know here in Australia if you want to get a .com.au address you have to have an Australian business number or be registered as a not-for profit in australia (same for .org.au and .net.au, with variations on the restrictions) . I know that .org also has similar restrictions - you essentially have to prove you're an organization in your respective country.