I am sure that someone else will give a more detailed response, but the short answer is that the Spanish destroyed most of the Mesoamerican codices. Also, the climates of Mesoamerica don't really facilitate the preservation of biodegradable objects like paper very well, so anything that wasn't destroyed by the Spaniards decayed fairly quickly after they were abandoned by their authors (it is important to keep in mind that something like 90% of the native Mesoamerican population was dead soon after Spanish contact). What we are left with, the Borgia Codex for example, survived to modern times largely by chance, often discovered centuries after their creation in people's private collections.