Like the Dark Brotherhood, thieves guild, Companions, etc...in Skyrim or will it just be "rescue kidnapped settler," "clear ___ area of all hostiles" and so on forever? So far it just seems like the randomly generated quests from Skyrim that you get when you complete the faction storyline.

Those are the randomly generated quests.

How do I get the main quests? I've only ever gotten the retaking the castle one for the minute men (which was the only one that seemed like it had any kind of story to it), the ones with H2-22, and like 5 doing random tasks for a quarantined safehouse for the railroad. It's become so boring and tedious and I don't know how to progress to something with substance.

The last Quest-Quest for the Minutemen after retaking the Castle is finding an old woman in the Castle who teaches you how to build Artillery.

After that, the only main quests are the Endgame against the Institute and if you turn against the Brotherhood of Steel.

Faction quests are tied to the story

Oh...well that's disappointing! I wasted so many hours doing this stuff hoping for something to happen, I'm an idiot >_<

Not necessarilly. If you want the Minutemen ending, you need to have 8 settlements allied to the Minutemen, which the allied quests do.

That allows you to destroy the Institute.

Then you need to build five pieces of Artillery.

Or more.

That allows you to destroy the Brotherhood of Steel.