If you wait to see a ripple, it means the fish is near that spot. If you click on the ripple, you should see a fly be cast, and a fishing line appear when it lands. The rod will flex when you get a bite, and clicking and dragging to the right will reel the fish towards the rod.
Clicking the water is a shortcut to equipping the rod, and clicking on the sky is a shortcut to unequipping the rod away. I think this needs to be added to the tutorial somewhere, I can see how it's confusing right now.