Yes in my opinion PayPal is the best, most well recognized, and secure way to accept payments from your customers for your eBooks.
PayPal does have some small fees associated with it but those fees are more than made up for in the security that they offer your users while they make their payments. I have been using PayPal for over 10 years and it is a great service. It is easy to use very reliable and has pretty good customer support if you need that. I have only had to use their customer support one time but the matter was resolved quickly and accurately.
But the more important aspect is the confidence they give your customer while using their service. PayPal is a well recognized and well respected payment gateway. Others have tried to compete but PayPal is still number one. They secure the customer payment information and it never leaves their control. You as a business never see what the customer used to make the payment. You receive the payment, almost instantly, but as far as the customer information, credit card number, bank account number, etc, you never have access to that information. I like that much better and I am certain my customers like that much better. After all making purchases on line can be a pretty scary thing in this day of hacking and the better the information is secured the better it is for my customers.