stupid GPS question

OK I am just getting into the VFR GPS navigation thing. Here is my question:
what is the origin of all of these intersections? I see some as airway
intersections on sectionals, but many seem random.
And why is it when I file an airway flight plan with AOPA flight planner, it
always throws a couple of these in the route? Why not just go from the last
VOR direct to your destination airport? Does it assume that I have a GPS
with a current database? Or is it assuming that if I am creating an airway
route that I am IFR?

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Hello, my name is Mike, and I am an airplane addict....