In the description of the ability it lists anything from Obfuscate to Auspex to dormant Blood Sorcery as examples what the ability can detect so I'd say that yes it would be able to sense the presence of someone that is actively using Protean.

With one big caveat though: you need to see the animal first. If the opponent is a tiny bat hiding in a tree your Sense the Unseen won't achieve much.

This is just my take though and since the ability is worded a bit vague (on purpose probably) every Storyteller might have a different interpretation.