Nowadays if you're a merchant selling online you have several options for accepting payments. You can either opt to go with a third party service (popular services are Paypal, 2checkout and countless others or you can go with a real merchant account of your own with a payment gateway). As a merchant services provider we run into merchants all the time that would like to build their entire business around third party services for various reasons, a couple are:
1. Third party providers typically offer bundled solutions at lower monthly costs.
2. Third party providers often offer easier setup for merchants without a merchant account history.
The reason for the easier setup and bundled solutions is simple, a third party provider is essentially someone that's using their merchant account to allow you to accept credit cards. Consider it a "friend" that's allowing you to use their account, in their name to accept credit cards. So they're able to offer a slightly lower monthly fee (typically only around $5-$10 per month lower to be honest), than a traditional merchant account. This seems attractive to smaller merchants initially, but smaller merchant should consider that third party accounts don't do much at all to benefit your processing history. Since you don't have an account in your name, you have nothing to take with you once you've been processing cards with a third party provider for 2 years and decide to open a real merchant account of your own (if you decide to open a real account or even open a retail/mobile operation). Another important note to consider is that your third party provider's name will appear on your customer's statement and you may have to remind your customers that the name "XYZ provider will appear on your statement" just to keep them from disputing that charge.
A myth is that merchant accounts in your name are difficult to setup; in many cases today merchant accounts are as easy to setup as third party accounts as bank/processor underwriting departments have gotten better and faster at verifying information. Merchant accounts are similar to credit and should be treated as such, the better you avoid fraud (as best you can), the easier it is to move on down the road and receive even better rates as an established merchant. Also, be weary of the "lower rates" that many third party providers offer, a third party provider may charge nothing monthly to accept cards from your website but if you decide to offer mail/phone order capability, several popular third party providers charge $20+ per month just to add the virtual terminal capability which allows you to punch in credit cards manually.
Finally real merchant accounts usually offer superior customer service (phone, email and web) as "registered" Visa/MC providers are backed by huge banks and are held to higher standards.
In some cases if you're smaller and don't mind lesser electronic payment acceptance options third party providers are better. But if you're looking to build your business and build your own merchant "file" you may want to look into opening an account of your own.
As with anything it depends on your business model along with the options you're looking to offer your customers.
