Should I Book Flights With Booking.com?

Ever since I was born, I have always booked flights with the official airline site, and I fly multiple times a year, both abroad and domestic. I mostly book flights as well as chain hotels on their official site as I was quite skeptical of using [booking.com](http://booking.com) to book flights, chain hotels, and car rentals even though I used [booking.com](http://booking.com) to rent smaller boutique hotels or temporary Airbnb-like apartment rentals and had no issues with these. This year however, I have seen that [booking.com](http://booking.com) only charges $334 for a flight from Boston to Lisbon whilst Azores Airlines charges 414 or something, so I am wondering if I should take the plunge or I would regret it.