I'm working on a business-oriented startup that requires credit card transactions, and part of my desire to have payments on my own site is because of the signal it sends out that you have your stuff together.
You tech people keep forgetting that reading a URL bar requires superpowers. I guaranteed you, having suffered many customer support incidents because of this: many people cannot tell the difference between getting redirected to Google/Paypal and the site they were originally on. (For that matter, a huge portion of my customers don't understand that I am not Yahoo or Internet Explorer.)
You may feel different about it but the average person doesn't.
Given that PayPal has more established accounts than Checkout or AMZN, my assumption is that those services would get even less.
I understand business' distaste for co-branded UI; it can be a jarring experience for users and it often feels unprofessional.
That's one reason.
Second, anyone who's ever been screwed by PayPal or Google Checkouts (they stole my money without warning) is going to be wary of it.
I know that for my own online shopping, I'm much more likely to purchase from a site that uses Google Checkout or Amazon payments than on that wants me to enter my CC information onto their own page. I figure Amazon already has my CC info anyway, and Google is more likely to have sophisticated security measures than joe-random ecommerce site.