Many of the larger companies have the capability of paying by direct deposit but many of the companies we work with are small 'mom and pop' type outfits for whom PayPal is a step up from handwriting checks to shoppers and putting them in the mail.
Some companies send money through PayPal from their credit card, which also means they have some 'float' time on the money while they collect and clear payments from their clients, just as I pay for shops by credit card wherever possible to have 'float' time while awaiting payment. Direct deposit requires you have cleared funds available to be sent. Checks had best have cleared funds to cover before they are mailed.