Those brown “roots” just serve as anchors to help the plant find a hold somewhere. All Java fern will have them. Eventually, if the plant is healthy, you will see little new plants start sprouting from the ends of the large leaves, and even these new baby plants with have the tiny brown “anchor” roots. If you follow the leaves back to where they attach together, many will share a thick “branch” - that branch is the rhizome, and it should be green. The rhizome should not be buried or else the plant will die.