zero-G planes are only mostly zero-g. They fly a parabolic trajectory, so their body actually rotates about the center of mass while flying.
Also, their weightlessness is not as well controlled as a drop tower's.
The cost you've listed is for a single passenger.
You know what's more expensive to build and operate than a pressure controlled tube on the ground? A pressure controlled tube with jet engines operated by pilots.
That's still expensive, but not outrageously so.
According to Wikipedia, they need 90 minutes to evacuate the tower before every experiment. Does an individual experiment involve multiple (dozens? hundreds?) of falls?
I'm assuming they have a long list of people who want to book time in the tower.
Regarding acceleration and deceleration, it's not as bad as it sounds/looks. Most off the shelf component will easily survive, provided you fastened them well enough. Rule of thumb: If it survives shipping by parcel service, it will survive the tower ;-)
Let's say the drop tower is open 9am-7pm Monday-Friday, so 10 hours a day, for 5 days a week, and 50 weeks a year. That's 2500 hours of drop time a year. Let's say the building can be expected to last 100 years (probably lasts much longer, it's solid concrete after all) and cost 20 million dollars to build. Thus, you get 250k hours of drop time for $20MM, so each hour of drop time costs $80.
[edit] whoops, turns out it's only operational for 30 seconds a day! That makes the price go up about a factor of 1000, so the cost is now roughly $80k per hour.
Let's say you have a vacuum chamber (usually required for zero-g experiments) that takes up 3 seats, and you pick the cheapest zero-G flight I could find at $5000 for one flight, 15 periods of 20-30 seconds of weightlessness each (let's say avg 25 seconds.) That's $15,000 for 375 seconds, or 0.104 hours. So your hourly price is $144,230.
With the revised math, the tower still wins, $80k to $144k, but I'm surprised it can only drop three times a day.
The drop tower does not allow things to be dropped for 10 hours each day. There are only 3 drops per day, so each day gives <30 seconds of drop time.
If you want to get in and have a trip, it costs around $5-10k. So judging by this price, it doesn't seem that the expense is high enough to justify building an apparatus that looks quite expensive.
I'm sure that there is a very good reason for drop towers to exist, I just don't know which one.