The short answer is: launch costs and crap rockets.
Building a big ship, right now, means lifting lots of mass into orbit and assembling it there. That in itself will be stunningly expensive. But then you want to actually send it to Mars.
Earth orbit to Mars orbit costs about 6 km/s (see http://i.imgur.com/SqdzxzF.png), which is comparable to the 9.4 km/s needed to get from the surface of Earth to low earth orbit. Now, we are in space, which means we can use slow, efficient burns rather than the fuel-belching behemoths you need for a launch... but right now we're limited to inefficient chemical rockets, which means a hell of a lot of fuel.
The ISS masses about 400 tonnes. Assuming hydrazine as a fuel, with an isp of about 350, that means that the wet mass of your vehicle has to be (dry mass) * e^(deltav / isp9.8) = 400e3 e^(6000 / 350*9.8) = 2300 tonnes. So you'll need 1900 tonnes of fuel. That's 380 Falcon 9s full of rocket fuel. (Assuming my maths are right.)
So you try to make your spacecraft as small as possible. That way you don't need to carry the fuel needed to move the fuel. The rocket equation is a bummer.
(Of course, nuclear engines, are vastly more efficient, change all this. Shame we don't have any. If you were willing to wait long enough, an ion thruster with an ISP of 20000 would require only 12 tonnes of fuel. But you wouldn't live that long.)