What is the difference and why does it matter in the Oregon situation?
Let’s start with the word “militant”, which conjures up visions of ISIS, Al Qaeda, Boko Horom, and other militaries trying to control the world and injure as many people as possible. According to Merriam Webster a militant is defined as “engaged in warfare or combat :” a militant person. 
Why is this so important in the Bundy situation at the Malheur Wildlife Refuge? If the President can get everyone to address those at the refuge as militants, then the President can use drones to kill off those that will not comply as per this article, “The Obama administration, Holder said, rejected the use of military force where “well-established law enforcement authorities in this country provide the best means for incapacitating a terrorist threat.” But in theory, it’d be legal for the president to order such an attack under certain circumstances, Holder said.”
Militia is defined my Webster as: “: a group of people who are not part of the armed forces of a country but are trained like soldiers”. 
Cornell Law defines militia as: 10 U.S. Code § 311 – Militia: composition and classes
“(a) The militia of the United States consists of all able-bodied males at least 17 years of age and, except as provided in section 313 of title 32, under 45 years of age who are, or who have made a declaration of intention to become, citizens of the United States and of female citizens of the United States who are members of the National Guard.
(b) The classes of the militia are—
(1) the organized militia, which consists of the National Guard and the Naval Militia; and
(2) the unorganized militia, which consists of the members of the militia who are not members of the National Guard or the Naval Militia.” 
Militia then is a group of individuals who are trained like soldiers, but not part of the military. They can be called out by the county sheriff to assist in the community should there be a need for them, to help secure and protect. If for example there is a small disaster in the county and the all of the police, sheriff, and deputies have already been dispatched, but help is still needed, the militia would then be called out. Then should more assistance be needed the governor could call in the National Guard.
The patriots in each state would be the 3%, the Oathkeepers, and others with different names in other states such as the Pacific Patriots Network (PPN) in the Pacific area of the country. The mission statement of the PPN says, “”The mission of Pacific Patriots Network is to provide a comprehensive and integrated response that coordinates community resources to protect life, liberty, property and the environment of our communities through mitigation, preparedness, response and recovery from all natural and man-made hazards that may impact our communities. We are our communities first responders.” 
As you can see, the terminology used by the President, the main stream media, and others who report the news of the Oregon situation can determine how those patriots and militia who were there to fight for the rights of all Americans are thought of. The fact is that once the media started calling them “militants” they put them on the wrong side of the situation and deemed that people should hate them, when the reality is far from that. Those people were there to fight for the rights of not only the ranchers who were having their land stolen by the BLM according to their reports, but to fight for every American to own and keep their land protected from the federal government over reach.
 Merriam Webster definition of “militant”, “engaged in warfare or combat”, http://www.merriam-webster.com/dictionary/militant
 Eric Holder: Drone Strike To Kill U.S. Citizen On American Soil Legal, Hypothetically
 Merriam Webster definition of “militia”, : a group of people who are not part of the armed forces of a country but are trained like soldiers”, http://www.merriam-webster.com/dictionary/militia
 10 U.S. Code § 311 – Militia: composition and classes, https://www.law.cornell.edu/uscode/text/10/311
 Pacific Patriots Network Mission Statement, http://www.pacificpatriotsnetwork.com/about.php