No scene should ever be about what it's really about.
To put it another way, consider an iceberg.
Text, subtext, context, metatext
Scenes are like icebergs: what's above the surface is only 10% of the total mass of the iceberg. A scene, and a story as a whole, should be the same.
Hooray for creative commons!
Anyway, I think a lot of subtext starts out as text, and during revisions you are able to help it slip under the water to give your scenes power. That's certainly been my methodology.
There are times, though, when you can let the whole text dip under the water, and that's when you're in trouble. That's the problem I've had lately: finding that equilibrium. I think I've found it now, at least for my current problem area. Time will tell.