The prestige also accrued because it was the language of the educated in Europe for a long time.
I was going to answer with just "the church" but the OP specifically asked about academia.
A good analogy is French being the language of the elite in Britain, well after the Normans got merged into the general population.
Why do you think all animal species have a latin name? You think the ancient romans classified them?
Edit: Re-reading I realise you were reading that as me thinking the books weren't written in Latin, whereas I was trying to get the parent poster to think a bit beyond "the books were written in Latin" to wonder why they might be written in Latin long, long after the fall of the Roman Empire.
I don't really care to waste my time since you don't really seem interested in learning anything new. Have a nice day.