So my idea for Chocobos is a little grand and complex...
So instead of just a means of transit imagine that chocobos acted as a mount that were an extension of your character. So just like a PC, a chocobo could go from active to passive mode and receive monster aggression. So even on a chocobo, you would not be safe. Imagine in addition to whatever personal chocobo system is in place there was a means to also level your chocobo up by engaging in battle and maybe even special chocobo based battle leves.
Now for means of transit, maybe the level of the chocobo would be decided by the location it is rented from or amount of gil payed. So from one of the starting cities let's say that maybe only level 10 chocobos are available to rent while at a camp like Bluefog they might offer up to level 40 chocobos for an increased amount of gil.
Traditionally chocobos have been a safe means of transit for Final Fantasy games. But I think the feeling of being like a chocobo knight or even leveling your own bird would be worth a little bit of danger while travelling.