Trent, do you realise that in many cases Skyscanner will actually take you through to the airline to make a direct booking? It's just a search tool. Not that it really seems to matter whether you book direct or not, especially with hotels. My parents swear by phoning the hotel yet always get the room they paid for and always pay more than they need to. I book with whoever offers it cheapest and have had countless upgrades.
With the airlines whatever cabin you're in the crew have no idea who you booked with.