We have to fix our roof next year.
It's leaking because we have a hole in our roof.
Please clear the snow off the roof by noon.
The root of your roof is still your roof. If it helps, imagine roots growing out of your roof. They protect you from the rain.
This word uses the kun'yomi readings. The kun'yomi for 根 is ね. For a mnemonic, we'll use the sound a horse makes, neigh (ね). Why is the horse neigh-ing? It's stuck on the roof.