According to a Navy release, Muslim Sailors aboard the USS Harry S Truman were able to celebrate the end of Ramadan while on their cruise.  The US Navy followed standard policies on religious accommodation, and provided meals especially for the observant Sailors, as described by the Truman‘s Chaplain:

“Whatever a person’s religious background, the Navy’s policy is to accommodate that person’s religious needs,” said Cmdr. Jerome Hinson…”We are able to arrange meals for them before sunrise and after sunset. Depending on their work schedules, we accommodate their needs as much as we can.”

The Sailors themselves spoke positively about the Navy’s support of their religious practice:

“It’s a great experience to be able to practice my religion here,” said Petty Officer 2nd Class Jason Jenkins, aviation ordnanceman, a Muslim sailor from Strike Fighter Squadron 32. “It really shows the commitment the Navy has in allowing us to practice our faith and that we are supported by everybody.”

In fact, the Muslim lay leader on the Truman, Petty Officer 1st Class Abdoulie Jallow, was sent on an official training mission to Mecca, which allowed him to complete his hajj — while being paid by the Navy for the trip:

Jallow said he was able take part in a joint-service training mission to Mecca to fulfill Hajj, another Pillar of Islam. As a trainee in the Islamic traditions and faith, Jallow said he was humbled and honored that his career as a sailor enabled him to fulfill a major part of his religion.

Whether one agrees with a particular religion or not, it is evident the military does not disfavor Islam, or any other religion, when practiced by its servicemembers.

The right to free exercise, regardless of faith, is one that is protected even in the US military, to the extent mission requirements allow.