Congratulations, you got the answer right, it is Antlion.
Twice Your Protector - In FFIV it was the protector of the Sand Ruby? Which you needed to save Rosa, and in FFIX, it was sort of a protector to Cleyra. In all you meet it 3 times, but twice it turns against you after being Tame.
Three Times A Foe - In regards to the Royalty bit, you fight the Antlion 3 times as a boss fight. (People may say that he's been a boss in more than these ones, but in the other games he was a "mark" boss (optional))
Each Time Met Royalty - Edward, Krile and Puck as Turk says.
And Would Not Let You Go - Boss battle / can't escape.
You May Misunderstand Me - In FFIV and FFIX the Antlion was a tame creature that was said not to hurt anyone.
My Guardians Say The Same - Puck and Edward both mention that it is tame.
But If You Research Me -
You'll See In My Fame - Reference to the fact it's been in pretty much all FF's bar a couple, but you needed to research the various few to match it with the riddle =)
Grats Turk. your go :P