Pope John Paul did not mince his words - he never conceded that Islam was on an equal plane as Catholicism - only that discussion should occur. This author was deceptive with his quotations on that issue, as well as in any implication that the Pope believed Islam stood with rights equal to Judaism as far as Jerusalem is concerned.
This should not suprise. The author is Juan Cole, a semi-famous (at home) tenured professor of something or other noted for his self-promoting fatuous fatwas.