Not that many breakfasts are cooked (it's hard to precise when exactly I'd use "gotować", but rather for lunch food), so "robić" (to make) is safer. Robię kanapki (sandwiches), robię naleśniki (pancakes), and even for zupa, which is definitely "cooked", 'robić' still works -> I'm making the soup".
Tough to answer that - you do cook them (frying is cooking still). I a not arguing, just asking because people here (I live in Poland) do say gotuje for things like scrambled eggs
I would never say that about jajecznica, although yeah, I found some results in Google for that. Still, we decided to accept English 'cook breakfast', but not Polish 'gotować śniadanie'. Even if some people say that, it seems totally non-standard.
From a native English speaker's point of view, "making breakfast" perfectly describes the process of preparing breakfast, whether cooked (porridge, eggs, bacon, toast, etc.) or uncooked (fruit, cereals, cold meats and sliced vegetables, etc.)