I'm on rural Suffolk at the moment, but I've never been anywhere else so it's hard to compare it to what it would have been had I lived elsewhere.
The main issue, like a lot of people said, was transport. If I wanted to see my GP while I'm here I would have to either use the very poor bus service (four busses a day with a choice of either returning within half an hour or four hours), walk along a very busy road where most people speed and there's not always even a grass verge to the town, or rely on my grandparents. Not everyone has grandparents, and mine hare bigoted and homophobic, so I doubt they're particularly trans friendly either. My other alternative would have been to bunk off college and get the train back to my own to see the GP when I should have been getting an education. Not the best of options.
Having a lack of facilities in the area. I don't know if after the recent changes they still insist on CAHMS giving you the all clear to be referred to a GIC, but that was one of the main reasons I haven't transitioned yet. My CAHMS doctor, who I was seeing for other reasons anyway, was a complete and utter sadist. He would talk this airy fairy nonsense, make assumptions that were completely illogical and wouldn't take being corrected, and I would leave feeling suicidal after going in relatively fine. My school nurse who attended a lot of the time actually rang me when I got home a couple of times to check if I was okay. The only time he was happy was when I was raging with anger at him, and started talking patronising bs about how if I was younger he'd put a teddy on a chair, call it Andy, and tell me to "shout at the Andy why I hated him." Maybe just ask? My parents, my GP, my school nurse and me all thought he was doing more harm than good, and he admitted he couldn't help, but as I'd been hospitalised after a suicide attempt a few month before they couldn't let me stop seeing everyone altogether. The shrink wouldn't let me see anyone else either because if he couldn't do it, then none of the more junior members at the centre could. Luckily, he wanted a 11 people meeting to discuss it, which we cancelled because we didn't agree and I slipped through the system and we never heard from him again. I've not dared go to a doctor since.
How did all that relate to being rural? If I had lived in a larger area, the chances are there would be more than that one centre who could deal with minors, and I wouldn't have to have suffered that toss pot. Maybe someone would have even reported him if he was exposed to more people (I didn't because I just wanted out at the time, but now I wished I had because of how awful he made me feel), my friend who was going there for EDNOS met him once at a weigh-in session, and she immediately knew who it was although she never heard his name. She disliked him, and she's much more tolerant of people like him than I am.
Everyone knows everyone is a big thing too. They'll all know my business, and the chances of me running into someone I knew if I did use the male bathroom would be high, and awkward.
I don't think education should count as a rural issue, because it's prevalent everywhere. I know trans people in a city in Scotland who were hounded out of a LBGT group for being trans, and they're not really marginalised there. They're both white in a white majority area etc. We had a speaker in to talk to us about sex ed (we were mostly 16+, a bit late for the majority in that hall...) and she grouped the T with the LGB and didn't explain one was sexuality and one was gender identity. It was her job though, and she works in the cities too, so it's not a rural problem, or at least wasn't for me.