DH and I travel with our meds as many have said above: controlled substances in original pill containers and other pills and vitamins in day by day containers with extras. We have flown 20 or more times in recent years and never had a problem or been questioned BUT.....
My sister who has MS has had 2 experiences that point out what can and does happen sometimes.
Her first flight to Florida she was having one of her bad spells with MS and was extremely sleepy; could not stay awake and asked to use a wheelchair once she got to Orlando. It wasn't meds causing her sleepiness but since she hadn't indicated needing a wheelchair at the gate it caused some questions I guess. A flight attendant (we think) alerted for the wheelchair and once she got up to the gate a security person stopped her and asked her several questions. She was asked if she was okay and questions about any meds and had to explain her sleepiness. Eventually she dug out her scripts and was allowed to move on. All of this she says was done very politely but seriously. She now carries a letter from her doctors stating that she has MS and what she takes.
Another time she was in a car back home, not driving and they were stopped for a minor traffic violation. I don't know all the story, but every person in the car ended up being asked to get out of the car, show ids and when she opened her huge bag (purse) some loose pills fell out. To say my DS is disorganized is an understatement.....but, she did find the pill bottle they belonged to. The driver, her husband who does carry many controlled meds for a severe spine problem wasn't even asked to show his meds! We still remind her to be sure to carry her pills properly when she travels with us though!!!
OT - Ironically, the last time we flew with my 85 year old mother she decided to take double her regular pain meds because she worried about discomfort for the return flight. She was totally loopy, talking crazy and could barely sit up straight in the wheelchair through the security lines. I kept nudging her to just stop talking and sit up straight so that Southwest would let her on the plane! DB and I practically strangled her worrying us about getting stuck in Kansas City overnight till she 'sobered' up. The security people though must have been too busy to notice her odd behavior, thank goodness! Never again!