It's simple: there's an expectation that some amount of due process has been done before granting you a merchant account. It's harder to setup than a Paypal account. Therefore it's more difficult for crooks/irresponsible people to get a merchant account than a Paypal account, therefore you look more professional with a merchant account.
Does that really go through a consumer's head at the point of purchase? Seems more likely that they'd think things like "ugh, not another site where I have to enter my credit card info - I wonder how trustworthy they are?" or if they're using a third party system like paypal, maybe they'd think "oh cool, I don't have to give out any personal info, I can just use my paypal account".
Just something to think about when setting up a payment system - you might want to grow into needing a merchant account system before you deal with the financial and logistical overhead.
" there's an expectation that some amount of due process has been done before granting you a merchant account."
Hmm. That's never occurred to to me when ordering stuff online. I do make a judgment about the reputation of the seller, but the payment method really doesn't figure into that unless it's something off the wall.
Barriers to entry can work for or against you.