Although they appear harmless, the leading cause of forest fires in Johto was once not Typhlosion or Houndoom, but Cyndaquil. It is thought that, unlike their evolved forms, this is because Cyndaquil are unable to control the flames on their backs, although some have viewed it as a deliberate manner to burn out and cook food, albeit one which comes as a high price. This has made the survival of young Cyndaquil difficult, and not solely because of humans; most predatory pokemon (and some who are not) are prone to killing and eating wild Cyndaquil not for taste and nutrients, but to protect their habitat from deadly fires.
Attempts have been made to domesticate the Cyndaquil, mostly for their cute appearance. They are docile in captivity, but have been banned by many cities for the exact same reason, especially cities made of wood. Although they're making a comeback in captivity these days, for trainers are better at handling them and towns less flammable than before, anti-Cyndaquil laws often remain on the books and their repeal is resisted by fire departments everywhere.
Indeed, some villages such as New Bark Town have actually passed these laws recently, spurred on by nearby fires and fear-mongering campaigns. The next day, Professor Elm gave his Cyndaquil away to a young trainer and started him on an amazing journey.