The Pope has said many positive things about Islam recently (as has people like Tony Blair, David Cameron, etc.). You get the feeling that this is almost politically compulsory in today's climate. In other words, far from “Islamophobia passing the dinner-part test” (as the then Baroness Warsi once claimed), the exact opposite is the case.
Perhaps the Pope is doing what Leftists frequently do: he's “lying for Justice”. (All politicians and activists, of course, lie at some point. However, Leftists – or at least Trotskyists, etc. – have a strong “theoretical justification”for it.)
The Pope may think that to believe – let alone announce - the alternative (that Islam is a religion of war and religious supremacism) is just too massive a pill to swallow.
In any case, some Christians, Leftists and interfaithers know full well that Islam is not “a religion of peace”. They know it as much as you and I do. However, to publicly pronounce that Islam is a jihadist religion will - they think - result in more communal conflict and violence, not less.
The truth is the other way around. After all, selling the lie that the Nazis “only wanted peace” in the 1930s meant that Britain and America lost a lot of ground when it came to destroying that particular enemy.
Interfaith gobbledegook and talk of Islam being the “religion of peace” (along with naïve and often politically fake pacifism) have led to more violence and bloodshed, not less.
What seems to matter more to these people (e.g., Leftists, interfaithers, etc.) is grandstanding their supreme tolerance and very deep lack of bigotry; rather than telling the truth. (Yes, they're being pious!) Thus some of them must know that lying about Islam is going to result in more oppression and death, not less.