Dealing with rusty bolts

What is the general consensus on using products like Never-Sieze on bolts?
I just removed the Fan, and all 4 bolts are pretty orange/rusty. Some other bolts as well.

I hit them with WD40 which helps a little.

What I am thinking is put a small dab of Brake grease on the threads. Thoughts?

Also just removed the water pump and water outlet, real rusty. ended up finding some heat resistant black bolts that will work. But would like to also lube them a little.
There was one bolt in the water pump that must be in water all the time. Maybe dont grease that one?

I also have 3-1 oil.