According to this article: George E. McCracken, "Nathaniel Foote's English Relatives", The American Genealogist, October 1977, Vol 53, pages 193-206, John Foote-43 was probably the brother of Robert Foote, the father of Robert Foote-35 and John Foote-72.
I just found an addenda to that article, in The American Genealogist in 1978, Vol 54, pages 99-101, 118-119, by Janice Green Valore, "More on Nathaniel Foote's Ancestors". It says that, "after considerable study of this Foote Family," "it seems highly probable that the earliest ancestors of Nathaniel Foote known were John Foote[-43] and his wife Helen or Ellen Waryn or Warren." and that brothers Robert Foote-35 and John Foote-72 were their sons.