I think this right here is a BIG reason why The Ship is more popular then Gmod Flood
On top of all of that, Flood is a gamemode for Garrysmod, so you have to buy Gmod in order to play Flood.
And since Gmod isn't as known as a lot of the "block buster" games out there, its easy to see, media wise, why The Ship is more popular.
I, myself, have only played Flood once and I got bored as I didn't understand the mechanics at first.
That was about a year or two ago.