You know what i think the difference is? Major gaming sites like newgrounds just have good looking ads, highly polished and fitted in the surrounding. The ads admob and friends include, look like someone just vomit in your game
I don't think they are good looking ads, its just as annoying as any other ads. In fact i recently was spammed on IGM with "this is not a joke, you're our 100,000th visitor and you win!!" flashing red/white banner like a crazy epileptic inducing episode.
Ads are annoying by default. We hate it in our mail, on TV, on the web, on mobiles.
If you the gamer hate it, then considering spending $0.99 to remove it or like some, just turn off internet or install adblock.
If its a big game and it doesn't have ads, you can be sure the IAPs are forced upon the gamer (Clash of Clans, Dungeon Keeper etc) due to the entire game designed around milking IAPs. Because devs need money to make games and it has to come from somewhere, if not advertisers paying for it, then gamers will pay for it.
I noticed Butterscotch Shenanigans in their early videos complaint how much they hate Ads as gamers so as devs, they won't implement it.. but then I checked their recent game updates, and they have Ads in it now. As they said, "we need to eat". Really, watch their presentation videos, you can see their progression from starting out as new indie devs to gradually realize that monetization is not separate from game design, that game devs are partially a salesman, but it does not mean you lose all respect of gamers. No, it can be done right.