I have flown with my machine on more than one airline. I put it in a bag that I paid less than $10 for at Walmart, it converts from a carry bag to a back pack. I take the needle out of the machine, put the presser foot down, wrap it in a piece of bubble wrap and put it in the bag. If I'm taking fabric with me, I will often put the fabric in the bag, around the machine, as well.
I have been asked a couple times to take the machine out of the bag but more often than not it goes through without a hitch.
I store it in the overhead compartment.