Changing a bike tire is not difficult, and is a lot easier to do than it was when I used to ride a bike to school. Even then there are may types of goo you can put in the tyre to automatically patch a hole should it happen. Bike pumps are a lot smaller than a drink bottle and normally clip to the bike, or would easily fit into a backpack. Again, in most cases you will not need to use it.
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.
