Will there be any issue if I want to assist the employee of the company I work for to book flight tickets by paying with my own Paypal account?. On top of that, I plan to charge a little bit of booking fee. It's not quite convenient for them to book online by them self & there are numbers of people flying overseas every years. Thanks.
Depends on the airline's policy for third party payments. Many airlines want to see the credit card used when someone else is paying for the ticket. You would have to check to see what the airline's specific policy is for payments by Paypal (or other means), there is no overall rule.
As for charging for your service, that likely would not matter, unless the country / state you live in has strict laws about selling or reselling travel services. The airlines wouldn't know about any additional fees you asked your co-worker for.
Of course if you hide the extra fee in what you quote your co-workers as the full airfare, they may get upset if they get a receipt or booking printout from the airline and see the airfare is lower than what they paid.