I think the rum ration was to keep sailors from freezing to death on watch.
I read in some book (maybe 2 years before the mast), the author was a non drinker, but almost immediately began drinking his ration along with the rest of the crew, saying it was the only think that would make nights survivable.
Also, once upon a time, beer was the only safe, potable liquid available as most water sources were contaminated.