Many find it confusing that in some places the Quran encourages peace, and in others it says to “kill the infidels.”
The Quran was not written in chronological order. It takes some sorting out, but when a particular surah was written is important. Mohammed wrote the Quran in two phases:
THE MECCA PHASE 609-622 AD
The period when Mohammed’s followers were in the minority and had to ingratiate themselves with Christians and Jews.
THE MEDINA PHASE 622- 632 AD
The period when Mohammed’s followers were gaining complete control over the lands where they lived. This period divides into an earlier and a later phase. The first part is transitional and the later phase is when Jihadism comes into play.
Mohammed declared that his later (Medina) writings nullified his early writings (Mecca) when they were contradictory. Suras 2:106, 16:101, 13:39, 17:86.
A good website on abrogation in Islam is http://www.meforum.org
We may say that true Islam is not represented by Mecca Moslems, but rather by the (later) Medina Moslems. In America our contact with Islam would be with Mecca Moslems. However, we need to see what Islam does when it dominates. For example, what freedom does Saudi Arabia allow Christians and Jews in practicing their faiths? Some say Moslem extremists are aberrant, not the real Moslem. But these fundamentalist Moslems take Mohammed literally. They may be the truest Moslems.
Christians are challenged to love all Moslems, but that does not mean that we ignore their motivations.