Because the climate wasn't hospitable.

The largest civilisations tended to have wide open spaces to farm and build. The peninsular is heavily covered in jungle and that limits settlements to rivers, and also expose people to malaria. Even until the 19th century, very few roads connected the interior.

When people think malaysia is hospitable, they just mean its warm. Ironically the inhospitability resulted in the low population count, which then meant that there were no large wars.

Same population? My Google gave really big differences between number of Mayan, Majapahit and (for example) Malaccan populations.