Protect can be used in a combo, as it's Combo type is Passive. Of course, you'd need to find another move to combo with it. Maybe Protect + Reflect or Light Screen to give three Pokemon the effect of both at Priority? Depends on ref interpretation.
As for examples of comboes, they're really context dependent so it's hard to give a list of popular/effective comboes. Usually comboes fall into three categories:
-A way to get a lot of damage in one attack (see: every Attacking move + Attacking move combo ever, more specifically Sky Attack + Brave Bird, Overheat + Overheat, etc)
-A way to get a non-attacking move to work through a Taunt (see: Shadow Ball + Will-O-Wisp, Rock Throw + Stealth Rock, etc)
-A way to get an attack/effect at priority (see: Extreme Speed + Giga Impact, the above Protect + Light Screen/Reflect)
There are a lot of uses for comboes depending on the situation, but an important note; unless you're in a situation where you NEED to use a combo to achieve your goal (for example, need to get a Burn through a Taunt, need to KO a Pokemon in one action), a combo usually isn't the ideal choice. In particular, in a damage race, 9 times out of 10 you'll do more damage using three standalone attacks than using one standalone attack and a combo. However at the same time, you could go attack - attack - combo and KO in one round, which you wouldn't necessarily be able to do with attack - attack - attack. Some food for thought! One last thing, if you ever want to know if a combo will work how you expect it to, the easiest way is to just ask on IRC; people are almost always around and willing to weigh in on whether the combo makes sense or not. Let me know if you want to know anything else!
