"just do it" means specifically, "so what if you won't be an olympic star, won't lose 200 pounds or win a marathon, won't become a millionaire, even if your attempts fail and you totally suck at something, if you truly are interested in it and have a passion for it, don't discourage yourself, just do it anyway." Life is all about showing up and trying.
I played for years with a singer-songwriter who was just awful - tone deaf, fairly dorky, lame songs, guitar strings popping out, pretty bad. We were booed on stage more than once. After a couple of years I couldn't take it anymore and I quit that band. Years later I saw him play and he was totally great, had a fanbase and everything, and had done several tours in europe where he got really polished.
He kept at it for years, learned as much as he could from everyone he interacted with, and eventually learned enough to start playing first acceptably, then actually pretty well, within his niche, and today he makes his living full time as a musician. He was simply incapable of was taking to heart all the negative responses he got. They kind of just bounced off of him, and he persevered. When I saw him perform, one of his songs was called "Everything Sucks", and it was specifically about me and the really negative attitude I always had when we used to play together. Fans in the audience cheered for the song and they knew the words. It was sort of a teaching moment about negativity for me.
Anyway that's what "just do it" means. It means don't let negativity get in the way of what you feel like doing.