What reason is that?
Plenty of large companies use PayPal. The ones that don't usually just can't accept the fees.
I don't think the fees are the issue - credit cards siphon off 3% or more, depending on your revenue volume and so on. AMEX had a very public revolt in Boston circa 1995 when small merchants objected to 16% fees on transactions. Paypals fees are in the same league, as regular credit cards, IIRC.
No, the issue is the arbitrary treatment of your funds. According to multiple reports from merchants I have read online, Paypals actions can only be described as capricious and irresponsible when it comes to resolving disputes. I.e. freezing a $10k Paypal balance over a $15 dispute with a customer. The arbitration clauses, etc. give customers and merchants almost no power, ensuring that Paypal gets to have its cake and eat it too. In comparison, the dispute settlement process for credit cards relies on much better established laws, case precedent, and accepted procedures. Thus, you have a much better idea how its going to end vs. Paypal where the outcome may be losing access to all your company funds for weeks at a time.
FWIW, I am not trying to cast credit card issuers as angels here. There is a reason that Paypal sprang to life. But its primary purpose was to become a vehicle that allowed micro-transactions on the web without the need for credit cards. It's grown well beyond that!
Last but not least, using paypal can also result in changes to merchant behavior. For example, Adafruit allegedly stopped using USPS for shipping due to delivery disputes that could not be resolved with Paypal successfully. As a result, they now only use UPS and FedEx, where there are allegedly fewer issues confirming that whatever was supposed to get there, did in fact.