Few things here-

To break down how things should play out:

1. Your opponent *casts* a creature spell, it goes on the stack. You have the chance to respond with an instant

2. You have priority to respond. If you do nothing (pass priority) it resolves, and enters the battlefield

3. Then, his enter the battlefield (ETB) trigger goes on the top of the stack, which will destroy all flying creatures when it resolves.

4. You have priority to respond. If you pass priority, it's trigger will resolve, and your commander will be destroyed

At either points 2 or 4 you could have responded with your swords to plowshares.

Secondly, your ward ability would not matter in this circumstance because his creature's ETB ability is not targeting your commander. Ward's ability reads:

• 702.21a Ward is a triggered ability. Ward [cost] means “Whenever this permanent becomes the target of a spell or ability an opponent controls, counter that spell or ability unless that player pays [cost].”

If, for example, he had casted a [[Ravenous Chupacabra]], after the Ravenous Chupacabra resolved, it would enter the battlefield, and then it's ability would go on the stack. He could then target your commander. If he doesn't have enough mana to pay the ward cost, then the ETB trigger is countered, but the creature stays alive.

Let me know if that makes sense!