If the haploid prothallium of a fern fertilizes itself into a diploid sporophyte, does this make all ferns clones?
No, it would not be accurate to label them clones, and the organism still goes through sexual reproduction even if they are selfed. Selfed offspring would get two copies of the "same" chromosome (when selfed within the same prothallus), when the parent might have two chromosomes of different origins, and there will also be recombination during meiosis (during spore production in the sporangia), which will alter the chromosomes. And even if all selfed offspring from the same prothallus will carry that same chromosomes, different prothalli from the same parent will carry different chromosomes, which means that all offspring will not be identical. So to label selfed ferns as clones wouldn't be accurate, since the offspring wouldn't be genetically identical to their parents and offspring from different prothalli would also not be genetically identical. The situation is similar to e.g. monoecious plants that lack self-incompatibility (especially those pollinated by wind), where selfing will be common. The difference in ferns is that all gametes on the same prothallus will carry the same chromosomes. 

Also note that some ferns have mechanisms to avoid self-fertilization, and that many species have a mixed mating strategy that allow both selfing and outcrossing, usually with higher fitness in outcrossed individuals.