When you look back at the last century, the consistent story is the pace of technological development. Just think. The Wright Brothers took to the air at Kitty Hawk in 1903 for the first powered flight. Today, the Airbus A380 would seat 525 people in the usual three classes of cabin space. But if it was economy class throughout, about 850 could sit and travel in relative comfort. So, in the space of one-hundred-twenty years, we've gone from no passenger over a short distance, to hundreds of passengers being taken more than 9,000 miles without having to stop for fuel. Although it wasn't always the case it is now remarkable that when you measure the number of passenger deaths per mile, flying is now the safest form of public transportation.
When flying started, it was considered too dangerous to allow paying passengers. Only slowly were the rich allowed to buy their way onboard. This was reckless of them, but there was a certain glamor to being seen to live dangerously. When you actually look at the conditions, the cabins were not pressurized and desperately noisy. Passengers were crammed together like the proverbial sardines in a tin. Ignoring the A380 experience which is still somewhat limited, all the cheap air tickets are in smaller airplanes and the seating experience is often cramped. It's a simple problem of economics. If you put the maximum possible number of seats in the plane, the cost per passenger is lower. If you increase leg room and allow greater width in the seats for the increasingly overweight passengers, the cost per passenger rises. It's the same aviation fuel cost and overheads divided among fewer people.
It is, in reality, no more comfortable to travel by air today than it used to be sixty or seventy years ago, which produces something of an irony. The only real advance has been in convenience. You're not shaken around so much and the noise level is more bearable. So the choice comes back to you. Cheap air tickets are always going to be less comfortable. Will you pay more to be more comfortable?