It's funny in a way because you can see the age old issue at work again: everyone wants something that's first rate, but they want to pay third rate prices for it.
Desilu really wasn't the outfit to be producing Star Trek.
It was a marriage of necessity when both really needed a different partner. Star Trek
needed an outfit with first rate facilities and not one on the financial ropes. That wasn't Desilu. Desilu needed hit shows, but ones that weren't going to cost them much money. They needed something more conventional. The problem with that is that something more conventional was less likely to be noticed amongst all the other programming.
Anyone should have seen going into it that a show like Star Trek
could reuse existing studio backlots and redressed props only so much and that a lot of stuff would have to be made from scratch and it would (by necessity) be f/x heavy. From a purely business standpoint it's easy to see how Desilu execs were not fond of Star Trek
particularly as many of them being old-school which likely wouldn't have found the show's concept appealing.
A show like Star Trek
simply couldn't be done cheaply.
Another thing to keep in mind here. Not being a runaway hit is not the same as being a failure. There's a lot of middle ground.