I've never experienced any glitches while traveling with pipe and tobacco within the US. Here's what I carry in a quart-size zipper bag:
+ Three or so garden-variety pipes
+ A labeled pouch or two of tobacco
+ Pipe cleaners
+ Disposable butane lighter
+ Box or two of matches (just in case)
+ Cheap pipe "nail"
All this stuff fits conveniently in the zip-loc bag, which can be packed and unpacked easily in an outer pouch of my carry-on bag (or messenger bag, if I'm traveling w/a laptop). Though I've never had to remove my pipe bag, I like to have it handy for inspection in case I have to go through a bag check. And since you have to pack liquids in a clear, 1-qt. ziploc bag, anyway, this routine is efficient.
I never take my regular pipe lighter with me - just take a disposable, which you can easily replace if you have to give it up or lose it.
I use the same set-up when I travel abroad. I've occasionally had to go through a bag check at European and Asian airports (maybe because of the tobacco or pipe tool - I have no idea). The ziploc pipe bag might get a glance from an inspector, but having everything visible and accessible makes it pretty clear that it's a legit pipe-smoking kit.