Put a few nukes on the Shuttle, and you can drop them anywhere in the world with much less warning time than intercontinental ballistic missiles. At least that's what I read about the reasoning of the Russians building their own shuttle, because when they ran the numbers on the Space Shuttle they concluded that a "civilian use" didn't make much sense.

Cargo capacity... Not that much really, since you're carrying yourself a whole lot of orbiter already. It had a large volume in the cargo bay, and the mentioned ability to retrieve things in that cargo bay.

But yes, DoD/military influenced the design of the Shuttle. It just turns out they never used the capabilities they requested. And so you end up with a craft that makes little sense for civilian use, except for the building of a massive space station in orbit and eventual servicing of satellites.

Consider that a large number of Shuttle missions were classified, then put two and two together...