These things happen from time to time even with the best contractors. I have been in both of your positions. If you have a long standing work relationship with the handyman and the quality of work and communication is typically adequate, pay the him what he asks. Once in a while, you run into complications that require a ton more work without much cost in materials.
For instance, that floor repair, it may have been a small area, but may have developed into a larger problem down the road. You could have thrown a bandaid on it and reglazed the tub at your desired cost only to discover that leak that caused the rotted floor would have resulted in the tub coming out next year. possible structure repair and maybe ceiling repair of the floor below with a new tub install and repair cost similar to what you are looking at now. He may have just saved you some money.
That minor floor repair may have been entirely more complicated than you imagine it to be. Often time it is difficult to cut the multiple layers of flooring out, Ive seen as much as seven layers of flooring under cement board and tile. Often the new repair needs blocking put in place. A handyman more than likely has scraps of materials for jobs like this. He may not itemize these extras and scraps in your materials costs along with various fasteners and adhesives. Even that tub surround you wanted installed, often the stud placement isn’t adequate for a proper install and requires $10 in materials that’s may result in several hours of work to get a quality install.
More to the point, if the guy does quality work for you and you have no complaints about the end result, pay the man. Preserve the relationship. The next guy may charge nearly the same and not take the time to go the extra mile and replace that damaged wood which was outside the project and was obviously going to add to the cost of an already unwanted repair.
If you are truly unhappy with the quality of the work pay him and move on. There is no upside to not paying him. He will talk to other contractors in the area and it will become harder for you to find good contractors.
As a former contractor, when I walked into a home, I was interviewing the homeowner as much as they were interviewing me. No one wants to work with unreasonable penny pinchers. Everyone wants to spend less than a repair is worth,but make waves and your costs will naturally go up on future repairs.