Travelling with medical equipment and a "special" disease takes a little more planning than just being able to "hop a flight" at whim.
When booking, tell them all about your needs. Can you climb stairs to get into the aircraft? Do you need the high lift? Do you need a wheelchair to get to your seat? Can you walk along the air bridge?
And sometimes, just when you think you have it all down pat, it will jump up and bite you in your butt! So MAKE SURE you have your bases covered!
Let them know what you are travelling with. BiPAP? Wheelchair? Mobility scooter? They will want to know the weight, measurements length and width and height. The type of battery. How many volts? Dry cell? Lithium? Get all of the information and keep it with your travel documents so you can just show them at the check in counter.
Shop around to get insurance. It is possible to get it, even if you have Pompe.
As I said above, MAKE SURE you cover your bases. This week (August 2012) I wanted to use my bipap machine on a flight from LAX to Auckland. And was told in no uncertain terms that my machine was not allowed to be plugged in to the medical outlet on the plane. This, despite my previously having been given permission to do just that. After about an hour of being made to feel like a sneaky little liar and trying to get them to let me plug in, the Captain finally gave his permission. It clearly states on this AirNZ website that my machine is approved for use on the plane I was on, and for use in the medical power outlet. So again, MAKE SURE you double and triple check so you don't end up in a tail spin.
NOTE: You NEED to have a lead with a USA plug for your bipap. Not a conversion plug, but a lead with the plug attached. Apparently the conversion plugs can cause arcing so they won't let you use them. I have also found that it depends on who you ask as to whether or not you can fly with a conversion plug, or the USA lead. As I said, make sure before you fly!