1 Most people don't use PayPal
PayPal has a large customer base, but the majority of people online don't have a PayPal account. The number of people who have credit cards far outnumbers the number of people who use PayPal. This can result in many lost sales.
2 Many people hate to register
Even when PayPal offers people the option to checkout with a card, they are still asked to register. Many people might not complete the sale because they are not interested in registering or signing up.
3 The checkout form is variable
The paypal checkout form can differ from one instance to another and so it might be impossible to prevent lost sales in many cases.
4 The checkout form is not customizable
Paypal's checkout form is not customizable. This can lead to lost sales and less customers. The checkout form only works well for people who have a paypal account.
5 Some countries are not supported
Not all countries are supported by PayPal, and as a result, a person who wants to buy your products from one of those countries won't be able to do that.
6 Account could be shut without warning
The PayPal account could be shutdown without any warning if they believe that your account is fraudulent. The account could also be locked down for a long period of time until PayPal feels comfortable opening it.
7 They hold funds for no reason
Paypal can also hold funds to do some reviews without giving apparent reasons. This can result in delays in receiving your money.
8 It can't be used alone
PayPal is just one payment option. Many people have credit cards and don't use PayPal, and thus using PayPal alone will certainly result in lost sales.
9 You might not be able to stop chargebacks
Sometimes disputing a chargeback and providing enough evidence results in nothing. The money is still taken from the account even if PayPal believes you. See also why Clickbank is bad.