My 2 year old has traveled four times by plane since 6 weeks old. We've purchased a seat every time except the first flight but were lucky to get to take her infant seat onboard and use a seat.
The only safety concern I can think of is if the plane hits turbulence. Just hold on to your son even when the flight seems to be going along fine. Planes can hit turbulence unexpectedly (it's happened to me on a few occasions) and people go flying in the aisles. If your son isn't secured in your lap, he, too, could get bounced around.
Even when purchasing a ticket, my daughter wants to sit in my lap on flights. I appreciate having the extra seat though so I can strap her in at least some of the flight. She wants to get down and run in the aisles, so it's difficult for me to keep her in my lap when she's ready to get down.
I've never heard about giving a toddler decongestant on a flight, but since your son has a history of ear problems, maybe that's why. My daughter hasn't had a problem so far (we're going again next weekend so I hope I don't jinx it!). We always have given her something to drink on take off and landing. I'm not sure how that will work now with carryon regulations, but we'll ask the flight attendant for something if we can't carry anything on-board. I think it's supposed to be worse on landing.
Good luck with your trip!!