Because Drogon was not in Meereen when she decided to chain the other two dragons and his exact whereabouts where unknown.
Following Daenerys' conquest of Meereen, Drogon, who is now the size
of a small ship, kills and eats the goats of a local goatherd. (...)
Dany is later dismayed to learn that Drogon has killed the daughter of
a goatherd. She tearfully confines the two smaller dragons to the
catacombs of the pyramid while Drogon remains at large, having last
been seen over the Black Cliffs.
Daenerys confides in Daario Naharis that she has no idea where Drogon
has flown off to.
Drogon is not less dangerous than his brothers, he's actually the most dangerous:
He is the largest and most aggressive of the three hatchlings.