How do I finish a main quest when I have to protect a settlement quest keep showing up?

So basically I am several hours already in Fallout 4 vanilla, over level 200, have too many legendary weapons and armor to count, modded everything and collected all the magazines and bobbleheads. I have just begun the main quest for the Institute. I have not yet betrayed the Railroad. The BOS are still at the airport but I have become hostile to them.

I am currently at the point where I am pissed due to me having to do a sidequest to protect a settlement, save a kidnapped settler and remove some raiders/gunners/super mutants sometimes protect from BOS. I can maybe do part of the main quest afterwards and another sidequest pops up.

How do I stop the sidequest from popping up while doing the main quest?

Do I need to turn off Freedom Radio?

Do I ignore them?

You can simply ignore those: they are repeatable events and nothing serious could happen if you fail them. For example, see Defend settlement quests:

Failing to provide assistance can result in damaged defense equipment, generators, crops, and/or a loss of settlers.

The chances of a raid are a function of your "Defense" stat at the settlement. There is a loading screen message that advises you to build so much defense per every food and water generated, but IIRC that is just a 'minimum suggested' guideline - having a much higher defense will continue to reduce the chances of a raid (I wish I had a link for this, but I can't remember where I read it).

If your that deep into the end game, just craft a bunch of turrets or other defenses and put them everywhere.