Yeah, "regularised" acronyms are generally decided on by community, whether world-wide, as in SCUBA and RADAR, or a more distinct community, say the Texting world with things like, lol, omw, swak, etc.
I always thought a good rule of thumb was that if it got a submission in the Merriam-Webster or Oxford Dictionary.
Also, another difference between FBI and JATO is that FBI is an acronym for a proper noun (gov't agency in this case) while jato isn't and proper nouns aren't allowed in Scrabble.