I booked a trip from us.megabus.com and when the final amount is calculated it shows a 'facility fee' apart from rip total and the booking(service) fees. What is this fee? I have done bookings several times with this site but this is the first time that I got this.
The facility fee, operation fee, facility maintenance charge, customer facility charge, passenger facility charge, etc. is a fee for the upkeep of a terminal or similar facility that the carrier is allowed to pass through to the customer.
You would think that this would be an ordinary cost of doing business that the carrier would absorb and factor into the ticket price. By unbundling these fees and passing them directly on to the consumer, however the fare portion of the cost is made to look artificially low, which makes the carrier look more competitive. It also helps insulate its revenue from discounts or other promotions that only apply to the fare itself.
This fee is extremely common for air fares and rental cars, though when purchasing airline tickets, it tends to be bundled in the quoted price along with all other taxes and fees, and in the U.S., airport fees are capped at $4.50. With Megabus, I suspect the charge covers their expenses in places like Boston or Washington, D.C. where they are required to use facilities in a terminal as opposed to picking up from the street.
Note that this is different from the concession fee, concession recovery charge, etc. which is the carrier essentially passing through their rent for operating space at an airport, bus depot, or other such facility where they may be required to operate.