Battery capacity is not related to the presence of a protection circuit. You can generally buy the same high capacity or low capacity cell with or without a protection circuit. Capacity is more a function of max discharge rate, with higher discharge batteries typically having lower capacity.
Also, you can't tell whether a battery is protected by the type of top it has. Unprotected button tops are commonly available (although I'm not sure you'd be able to find a protected flat top).
The largest capacity 18650 I'm aware of is the Sanyo NCR18650GA at 3500mAh. You can buy it in its unprotected form, or with protection added by various third parties. If you see an 18650 advertising a higher capacity than that, they're lying, it's probably a poor quality cell, and you should avoid it.
The good 18650 cells are made by Sony, Panasonic, Sanyo, Samsung, and LG. Try to find protected cells that are built from those.