I'm loathe to admit that I know such things, but Mr. Weber deals with the exact same issue in his Honor Harrington books -- stationary forts are a huge expenditure of men and material who could be fighting the war elsewhere. They're great if you know exactly how the enemy is going to attack... but they're a resource-eater when you don't.
In Wing Commander there are tens of thousands of jump points. In the game's Pacific War analogy, they're beaches -- and you can't build a major fort at every beach in the world.
Certainly, we see protected jump points... look at Pegasus in the Wing Commander movie or Ella in Wing Commander IV -- although in these cases the forts seem to be deployed to cover the entire *system*, blocking traffic from point to point. Systems are islands in our analogy, and you can't launch your Space B-29s against the next one until you've captured the orbitals.
There are lesser methods for protecting jump points... heck, a vast majority of Wing Commander is patroling jump points in fighters. We see minefields deployed, we see special buoys with armaments, we see manned turret mines... but in all of these cases there's an immediate response that negates doing it in the first place -- your minefield may slow the enemy advance down a bit, but it won't hurt them... they can push a minesweeper through.
At the same time, they're going to slow *you* down if you want to use your own jump point... so you don't deploy minefields everywhere and hope you won't need that point and the enemy will. (That is to say, you don't mine the streets of San Francisco because you're worried the Japanese might invade someday. You wait until it happens.)