What is he really saying..?

A slick word can not replace a firm footing. The longer quote may reveal a clearer message, but is it sincere? Regardless of fine words, actions remain the definitive assessment of true intent.

Actually what he said was very moving, in context:
"The future must not belong to those who target Coptic Christians in Egypt -- it must be claimed by those in Tahrir Square who chanted, "Muslims, Christians, we are one." The future must not belong to those who bully women -- it must be shaped by girls who go to school, and those who stand for a world where our daughters can live their dreams just like our sons.

The future must not belong to those corrupt few who steal a country’s resources -- it must be won by the students and entrepreneurs, the workers and business owners who seek a broader prosperity for all people. Those are the women and men that America stands with; theirs is the vision we will support.

The future must not belong to those who slander the prophet of Islam. But to be credible, those who condemn that slander must also condemn the hate we see in the images of Jesus Christ that are desecrated, or churches that are destroyed, or the Holocaust that is denied."

True enough...but why is the wholesale slaughter of Christians in Iraq and Syria NOT considered genocide? Why are muslims considered the only refugees?

It is considered genocide:
http://www.cbsnews.com/news/us-john-kerry-obama-administration-declares-isis-guilty-of-genocide/

Muslims are not considered the only refugees:
http://www.wrapsnet.org/Reports/InteractiveReporting/tabid/393/EnumType/Report/Default.aspx?ItemPath=/rpt_WebArrivalsReports/MX%20-%20Arrivals%20by%20Nationality%20and%20Religion

Actually, he does both at the beginning and the end of the quote when in context:

The future must not belong to those who target Coptic Christians in Egypt -- it must be claimed by those in Tahrir Square who chanted, "Muslims, Christians, we are one." (edit)
The future must not belong to those who slander the prophet of Islam. But to be credible, those who condemn that slander must also condemn the hate we see in the images of Jesus Christ that are desecrated, or churches that are destroyed, or the Holocaust that is denied."

http://m.christianpost.com/news/documentary-highlights-first-hand-accounts-of-irs-targeting-conservative-christian-groups-127212/ as the IRS Specifically targets conservative christian groups. I have a hard time believing what he says when the actions of his administration are the opposite.

http://m.christianpost.com/news/documentary-highlights-first-hand-accounts-of-irs-targeting-conservative-christian-groups-127212/

Actually the IRS targeted ANY groups which were applying for tax-free status that were likely not eligible for that status. There were a preponderance of such groups which were rightwing around that time because of the Tea Party and Kochs pushing to overload the system. They targeted any groups which sounded political, as political groups are not allowed in that tax-free category, and they targeted more conservative groups because many more were applying.
https://en.wikipedia.org/wiki/IRS_targeting_controversy