Aws vpc default route table in CloudFormation

Nah you can't, there's nothing to refer to anyway (e.g. logical ID). Just create your own main table ;-).

This is probably one of the reason it can't be used:

One way to protect your VPC is to leave the main route table in its original default state (with only the local route), and explicitly associate each new subnet you create with one of the custom route tables you've created. This ensures that you must explicitly control how each subnet's outbound traffic is routed.