I think it came from them not being used to the idea that the toys had direct tie ins to cartoons. That was relatively new at the time.
Revamping toy lines every couple of years when the "Story" was only in commercials was easy, because the kids didn't have a strong "group mind" emotional attachment to them.
One of the interviews on the DVD extras has a writer say something like, "I thought I was clearing space on the shelves for the next year's toy line, I didn't realize I was killing an Icon."
Yeah and on the Toys that Made us documentary about TF, they all flat out agreed killing off Optimus was a huge error.
An error that was compounded by bringing him back as Undead Optimus in Season 3, that episode was truly meant to make sure he was dead. He was never supposed to return.
Too bad though about Rodimus Prime, he certainly is demonized in the eyes of some of the fans these days.