Choosing a program is a personal choice based on many considerations. It sounds like you already figured out the first step - you want a FNP program with a goal of focusing on primary care. However, you also mentioned you live in a rural area. Are there any schools within driving distance of where you live? If no, you'll have to weigh the option of relocating vs attending an online program. This is not an easy decision to make. Relocation is not feasible for people with families and have already established a home (i.e., tied up with mortgage). Online programs do not work for people who learn better in a classroom environment and needs the face to face interaction with other students. Also, because online programs are based in locations that are away from the student's home, sites for clinical rotations are usually not arranged by the institution and the responsibility of finding preceptors are given to students.
What I have done as a former prospective NP student was to make the quality of my education as the priority. I was lucky enough to live within driving distance of a classroom-based NP program that is state-funded making me eligible for affordable in-state tuition cost and at the same time having the ability to have my clinical sites arranged by the school because of its close proximity and affiliation to major area medical centers. If this is not available to you and online is your only option, you can still acquire a quality education by choosing the right program. Some online programs arrange or offer assistance in arranging for your clinical rotation sites. You may have to go through a list of online programs and ask each program director how clinicals are set-up for their students. Avoid those that leave you high and dry when you start your clinical courses.
You may find the argument that the name of the school you graduated from does not matter to employers as true depending on where you live. On the other hand, you may also find that school name recognition gets you more interviews once you start your job search
. These are what if's that I worried less about, however, my primary concern was to make sure I get a high level of quality in my training so it became a given that I picked a good school though that does not necessarily mean a school name that is easily recognizable.