I paint my flex track using the cheapest hardware store squirt paint I can find. I use 3 colors, primer gray, any brown or boxcar red, and flat black. I paint everything before I lay it. Then I use acryllic paints from the craft store to paint the ties. I just slobber the stuff on, not really trying to make it look like anything. Lastly I pick out individual ties here and there with gray, tan or black. Clean the paint off the railhead as soon as it dries. Use a needle file to clean the rail ends so rail joiners can be added and soldered. Paint these areas by hand. I paint turnouts by hand, keeping paint out of the moving parts.
When the track is ballasted and scenery is added, it no longer stands out like a sore thumb, it becomes part of the over-all scene.
We tend to make our models stand out...they are the center of attraction. But just for fun, sometime, take a model car with you next time you go trackside. Hold the car at arms length, while you stand far enough away from the prototype, that it is the same size as the model. Note how the real trains blend into the background, totally ulike our models. Just a thought, Bill