You can use fertiliser to let one crop grow faster than the other ones, to get a double crossbreed in - thats the best use for fertilizing I can see.

Image you crossbreed Rare-Plant with Common-Plant. Both have a grow-time of 5 days, so normally they'd be ready to harvest at the same time. If you fertilize Common-Plant a few times it will be done before Rare-Plant, allowing you to plant more Common-Plant next to the Rare-Plant and giving you a second round of crossbreeds.
I'm currently growing both Mandrakes and Jute in my garden - MandrakeXJute is a cross that can produces new Jute-seeds, so I'll harvest the Mandrakes before the Jute and replant them, giving me 4 more chances per bed to get Jute-seeds!
(In this particular case mandrakes has a "natural" higher grow-rate though, so I dont need to fertilze at all costs, but you get the idea)

If you're not crossbreeding... fertilize as often as you like or fertilize if you want the product badly. (I remember logging in every hour only to fertilize the damn Thavnair-Onions when they were introduced because my FC-leader back then wanted them badly for his chocobo and kept nagging me... dont do that. Tell your FC-leader he can freaking do that himself.)