Lava,
You seem to be under the impression that there is a problem of Christians persecuting Muslims and that the Pope is somehow, if marginally, involved- and certainly insincere when he speaks regarding Islam. It seems like you have in mind a bigger picture happening here.
My point is that in Islamic countries there is a problem of persecution of Christians- I think arguably more so than of Muslims in the West. I think the Pope has good reasons, well aside from missionary reasons (which certainly both Muslims and Christians nurture), to speak of a need for peace and mutual understanding.