The AP uses the term "Muslim Majority countries" because the greatest percentage of citizens in the countries are Muslim. Your source is discussing not the percentages, but the absolute number of people in the world who are Muslim. For example, China has more Muslims than Syria although most people in China are not Muslims. See  http://www.pewforum.org/2009/10/07/mapping-the-global-muslim-population/ ,
I believe the AP term is still misleading because the seven countries in the original order were chosen during the Obama administration for enhanced security measures. It is unlikely the Obama administration selected the seven countries because they were majority Muslim countries. The new Executive Order ( https://www.whitehouse.gov/the-press-office/2017/03/06/executive-order-protecting-nation-foreign-terrorist-entry-united-states ) provides the history of the countries being put on the list, including the Obama Administration's reasons for each individual country.