Yes, but the bigger planes carry more than twice as many passengers. If we're talking about airport throughput efficiency of A380s vs Embraer 170/190s, the Airbus is going to win every time.
That said, most people want to fly point-to-point these days and not Hub/Spoke, and often _are_ willing to pay a few extra bucks to do it (I know I certainly will almost always take a direct flight if I can). This favours being able to use smaller airframes, and if it means avoiding a Hub airport it can be a lot more efficient. Where it gets dicey is trying to cram more and more aircraft through an already busy Hub. That leads to having to build more runways and doing things like double/triple simultaneous parallel landings.
That said, most people want to fly point-to-point these days and not Hub/Spoke, and often _are_ willing to pay a few extra bucks to do it (I know I certainly will almost always take a direct flight if I can). This favours being able to use smaller airframes, and if it means avoiding a Hub airport it can be a lot more efficient. Where it gets dicey is trying to cram more and more aircraft through an already busy Hub. That leads to having to build more runways and doing things like double/triple simultaneous parallel landings.