I didnt want to start using fertilizers but maybe I will have to. I currently only use Prime in my tank. The rhizome is the root system?
The roots are brown in colour; the rhizome is the part that the roots are attached to and will appear green. As mentioned, it should not be buried in the substrate.
Also, if you are noticing some brown spots, it is possible that it is all perfectly normal; Java Fern propagates in this manner.