Cave Story was an inspiration to the Indie Scene, a highly successful example.
But then again, there were many other games that did that just as well. Really it was the broadness of the internet that magnified the indie game scene, as well as the independent music scene, art scene, videotography scene, and the writing scene.
Pretty much without Cave Story there would probably be a little less of Indie action platformers, as in, a very little difference. Independence existed before it and would have grown without it.
But yeah it was one of the bigger influences, just not the ONE influence... I think I've made my point.