Fees for merchant accounts are like interest rates on loans - they vary depending on the perceived level of risk to the bank. Users of credit cards may refuse to pay certain charges for a variety of reasons, ranging from returned products to honest errors to fraudulent charges. Banks want to encourage the view of credit cards as a safe and convenient way to buy, so they are generally pretty lenient about allowing buyers to make chargebacks, as they are called. The risk to the bank, of course, is that chargebacks may occur after the merchant has already been paid, and the bank could be left holding the bag. How favorable a deal you get therefore depends not only on how large a company you have, and how long you've been in business, but also on what kind of business you're in.
Banks have stats on the rates of chargebacks and other hanky-panky in various different industries.
Banks do several things to limit their exposure to chargeback risk. They may ask you to personally guarantee the account agreement, meaning that if your company ends up owing money to the bank, you will be personally liable. Naturally, companies in businesses that have a high rate of chargebacks, especially those selling big-ticket items, will pay less favorable fees. Banks will also hold back a certain percentage of your money every month as insurance against future chargebacks. If you are deemed to be a high chargeback risk, it could be months before the customer's money makes it through the system to your bank account.