When I've travelled by air, "comfort" has never been the first thing to come to mind as I've shuffled through security, sans belt and shoes, hours before my flight's scheduled departure time.
I agree that there's a lot that's impractical about hovercraft - especially when for crossing the channel there's so much competition: ferries, the tunnel, and (as you mention) flying. For people who want to take their car across, as I understand it the hovercraft took about as long as the eurotunnel does now to cross the channel - but the tunnel has much more capacity.