I have flown with DD on 20+ segments since she was 9 weeks old and have always gate checked a stroller and many times have gate checked a carseat/booster in addition. I always gate check instead of checking in at the counter, less chance of damage. I have flown on AA, Delta, Southwest, USAirways. I use the JL Childress Padded Umbrella Stroller Bag, big enough for an umbrella stroller and you can fit other things in it! On our cruise I had a swim vest, sand bucket, & shovel in the bag with a Maclaren Volo.
On our last 2 trips DD sat in the airplane seat w/o a carseat (3 and 3.2 yo), but we used the 'Cares Flight Harness'. Pricey but we felt it was worth it, plus I know when DD is too big for it (44 pound limit) I will have no problem selling it on ebay or Craigslist. Once a child is in a booster, I believe most of them are not FAA approved for use in an airplane seat.
As for the clear bags... I have seen them given at Delta for carseats at the ticket counter. I have not seen them at the gate. I used to bring my own large clear bag (like a construction trash bag you can buy at Home Depot), then I bought a car seat travel bag on wheels. DD has since outgrown her travel car seat and I now use the Cosco Highback Booster for travel which comes in it's own clear travel bag instead of a box. I have never traveled with DD's normal car seat/booster, I refuse to lug a Marathon or Nautilus though the airport plus the last thing I want to do when I return to my car is re-install a car seat in 30 degree Boston weather in a snowy parking lot. I have always used an inexpensive spare seat for travel, plus it is nice to have a spare seat hanging around the house in the event of an emergency.