For me the reason is integration: Calendar invites, Google Docs "shares", and other permissions grants don't forward, so they always end up tied to the Google Apps account. Which means using it as a primary account, gives one a better more integrated experience.

I used to forward from my Google Apps account to regular GMail but different people would see my email address from my domain and others from gmail.com depending on their mail client.

It's a minor nuisance but switching it around and routing everything to my apps account solved that inconsistency.