We had a session yesterday (after a long break) and completed the second half of the "boss" fight for one of the books in an AP we're playing. We beat the fight, though there was a minor spat in the fight.
One of our allied combatants that was within the fight was affected by a Breath Weapon (a Supernatural Ability), and is considered immune to magic. This obviously encompasses Spells and Spell-Like Abilities. Reading the Supernatural Ability description, it states that Supernatural Abilities are Magical (which, in a literal sense, is to be of the nature of magic).
In the fight, we simply went with the creature taking damage from the Breath Weapon, and it didn't make a big deal since it has Resistance and a lot of HP anyway. After the fight, I re-read the description and for the particular specific entry listed, it limits its immunity to basically what I cited.
However, let's take a different creature (or even effect on another creature) that simulates this same effect, but without the listed limitation (for example, Anti-Magic Field). Would this then mean that the creature cannot be affected by Supernatural effects in addition to Spell-Like Abilities and Spells (and Magic Items)?
Supernatural Abilities (Su)
These can't be disrupted in combat and generally don't provoke attacks of opportunity. They aren't subject to spell resistance, counterspells, or dispel magic, and don't function in antimagic areas.
Magic immunity grants immunity to any spell or spell-like ability that allows spell resistance. Supernatural abilities (like most breath weapons) are not subject to spell resistance, and thus ignore magic immunity.
In much the same way, you can destroy a golem with acid arrow, because while it's immune to magic, acid arrow does not care about spell resistance.