I hike in the Grand Canyon once or twice a year and usually fly into Las Vegas, sometimes Phoenix. I've flown on various airlines - Delta, Spirit, AirTran, Frontier, Southwest.
I always check a rolling gear duffel. Hiking poles, tent stakes, stove and food are always checked. I don't do anything to protect my poles and have never had an issue, including CF poles. I carry on things that can't easily be replaced, DIY/modifed gear, favorite pieces of clothing, maps, etc. but, to be honest, I don't worry all that much. I do give myself at least one night on the rim before the hike in case I run into luggage problems.
I usually use my pack as the carry-on. You need the "frame" to be 22" or less to ensure no problems with carry-on size restrictions. I hike the Canyon with a GoLite Peak or ULA Circuit and they both work fine as carry-ons.
If you're hiking from the South Rim, the General Store in the Village has a decent gear section for last minute needs. Good selection of food as well. The one thing they don't carry are the small BIC lighters but TSA now allows you to carry those on. If you don't want to check any bags, you can also rent hiking poles at the General Store - $2 per day per pole as of last year.