Compared to a car, it's very cheap.
Flat tires... hmm: I average about one a year, maybe. It's not the biggest deal.
Are flat tires really that big of a barrier to entry?
Perhaps we should differentiate here between bike ownership and these bike/scooter share approaches. Scooters also have flat tires.
Compare ownership to a shared scooter or bike service, where these costs are in effect shared amongst everyone. If your scooter breaks down, you can leave it and seek other forms of transportation.
That leaves parking, acknowledged and your risk of having the bike stolen is totally dependent upon where you are and what facilities are provided. Many work places are seeing the benefit of fit staff and are providing bike cages in the corporate carpark. Same with shower facilities so you dont stink the office out.
There are many excuses you can use against bike use, but most of them boil down to it being something you are not used to doing and to do it you need to change your habbits.