I don't know if the US Military ever had plans for the space shuttle. I had a space exploration phase as a kid and I don't recall ever hearing that.
What I do know, however, is that when the space shuttle was unveiled in the late 1970s there was a mistaken belief that it was a military vehicle. Up until then space vehicles were capsules and these weird landers... nothing as recognizable as a plane. The shuttle was very plane-like and a lot of people jumped to the assumption that since it looked like a plane, and the military uses planes, it must be a military vehicle. The Soviets even had a mini freak out, thinking the US had developed an orbital bomber.
That it was basically just a space bus was established fairly soon after that, but the association of the shuttle vaguely with the US Military lingered.
The moulds that would become the G1 Combaticons were developed for Diaclone before getting released as part of the Transformers in 1985. So they would have been developed in the early 80s, when there was still a lingering "military" association with the space shuttle due to a misunderstanding of what it was when it was unveiled.
It's also worth noting that the Combaticons, Protectobots, Arielbots, and Stunticons were all originally intended to be moulds used in a Diaclone sub-line called "Limitless Combination." The Scramble City system would allow multiple mix and match options, so it's likely that originally having a space shuttle with the military vehicles wasn't seen as that big a deal since you could easily swap it with one of the jets if you so desired.
Of course releasing them as Transformers characters locked everyone into just combining with their specific team and sending the "limitless combination" aspect down the memory hole, meaning the shuttle was now locked into a team that didn't make a whole lot of sense.