The reason people are complaining (other than just wanting to use a gamepad on a PC) is that it is confusing to them since BioShock supported gamepads.
All the hemming and hawing about "WE WANT OPTIONS!!!" ignores the realities of game development.
The bit where BioShock used a controller when it was plugged in was probably a nightmare to implement and maintain, and added to the development, QA and support costs. Only to probably discover that most people never used it.
As much as people on that forum thread are complaining, they're probably acceptable losses. Especially since many PC gamers have demonstrated that when things don't go their way they'll migrate to consoles anyway.
Personally, I sort of dig that they're making the PC version with keyboard/mouse in mind. As opposed to id Software which is making RAGE with a gamepad in mind.
Don't get me wrong, I own a 360 gamepad and break it out when I play Street Fighter IV or racing games or others when it's appropriate. It's not appropriate for an FPS and it never will be.