Looks like nothing shuts down dialogue as quickly as the truth. Christians are persecuted in every nation in which Muslims have a majority (or even close to a majority). The Pope was merely speaking a word of encouragement for Christians to persevere. Once again, Muslim leadership is acting in a manner than affirms rather than obviates the suspicions that outsiders have toward Islamic violence.
Another Christian was shot and killed in Egypt according to this news report. It is not yet clear whether this was an act of persecution or murder. The shooter opened fire on a bus filled with passengers. It is possible that the bus was targeted because it was from a Christian village. The news report points to a number of issues creating conflict between Christians and Muslims. I think it is fair to say that Christians are not treated like other citizens in Egypt. There are significant distinctions in the freedoms of Christians and the freedoms of Muslims.