Hi,
I've worked both angles. I have my own merchant account and I'm a publisher with two accounts at clickbank.
The pros of using your own merchant account are:
1. Faster deposit of funds [usually 72 hours], sometimes 24 hours if you have a good merchant processor.
2. Lower fees. Again, depending on the processor range from 2% to 2.5% + .20 - .26 cents a verification
The cons of using your own merchant account are:
1. Customer service - You will have to process refunds. There is no way around it. Ultimately the customer can dispute the charge and you will almost always lose especially with a digital product. You can't easily prove delivery of a digital product unlike a physical product.
2. Chargebacks / Disputes . Visa regs allow for basically no time limit on a chargeback to be filed. I've had morons dispute a chrage almost one year later. You get charged $10-25 [depending on your provider] to receive a massive manilla envelope in the mail with the customer's complaint. You then have 10 days to respond or it defaults against you.
3. Unless you forward your customers directly to an internet based processor like Authorize.net , you will need your own SSL cert and order form. If you forward to authorize.net and use their SSL cert, You lose control over the order form's design. You can do some minor customization, but you lose out on most changes.
The Pros of using clickbank:
1. They handle disputes/chargebacks.
2. They handle the SSL cert / order form hosting.
3. Easy intergration. A noob can do it

4. large affiliate base
5. decent reporting tools
The cons of clickbank:
1. slow pay out. 2 weeks delay on checks

2. Insane fees for order processing
3. 10% rolling reserve [sometimes higher]