General antonyms:
* Recess: To set back or in.
* Withdraw: To move back or away.
* Retract: To pull back or draw in.
* Conceal: To hide or cover.
* Submerge: To go under water or be hidden below the surface.
Antonyms based on specific situations:
* If "protrude" means to stick out: Sink in
* If "protrude" means to bulge out: Hollow
* If "protrude" means to project: Recede
The best antonym will be the one that best fits the specific situation where you are using the word "protrude".