Where did the term "vegetative nervous system" come from?
"Vegetative" doesn't only mean related to plants, but has other less common meanings.


  4 a (1) :  growing or having the power of growing (2) :  of, relating to, or engaged in nutritive and growth functions as contrasted with reproductive functions a vegetative nucleus
  b :  promoting plant growth the vegetative properties of soil
  c :  of, relating to, or involving propagation by nonsexual processes or methods
  Merriam-Webster


So the word "vegetative" refers to the growth/nutrition functions of the autonomic nervous system. The short answer is that he chose that word because, particularly at the time he chose it, that was an appropriate word to use to refer to the regulation of things like digestion. Since the autonomic nervous system has other functions, such as in sexual arousal, and because the term vegetative has other meanings, the term "autonomic" has completely replaced vegetative in this context.