It's always the same. Someone says they had a setup done and it cost $100. Someone else says that they never pay more than $25. How come there's such a difference?
Sometimes you get what you pay for. If your luthier's rate is $50 per hour, do you reasonable expect that he will spend 2 hours doing a setup? And the answer is "yes" and "no". Depends on what he does in a setup. Here's what he might do:
1. Set the neck relief. Generally this is measured in thousandths of an inch. I certainly can tell the difference when I set up my bass with 10 thou or 12 thou relief. You need the right tools to do this and the patience to tweak and try for a while to find the optimum for the particular bass, the particular strings and the owner's playing style.
2. Adjust the nut slots. Not so critical a measurement as relief, but a lot more risky to attempt. If you mis-adjust the relief, you can always correct it with another truss rod tweak. Mis-cut a nut and it's a lot more trouble to correct.
3. Adjust string height at the bridge. Not a difficult thing to do, but can be fiddly getting a good match of the strings to the fretboard radius with a slight gradation of increased clearance on the lower strings.
4. Intonation adjustment. Here's where a lot of experience can be beneficial. New strings intonate differently that old ones. So if you set the intonation perfect on a new set of stings, the intonation has no where to go but to get worse as the strings age. Probably better for the owner if you deliberately intonate off a bit in such a way that the intonation will actually improve for a while as the strings settle in. And it's worth noting that intonation problems show up regularly on TB. Clearly not everyone understands intonation, how it works, what causes intonation problems, etc.
5. Pickup height adjustment. A proper setup will take this into account. There are numerous complications caused by pickups set too close to the strings or too far away. There's lots of room for personal taste here to, so the setup person must have a pretty good understanding of what you want from your instrument to do this right. You need to pay attention to the balance of overtones as you adjust the pickup height. Weird things start to happend to overtones once the pickup get close enough to the string to magnetically affect the string's vibration.
6. Check fret ends and dress as required - especially on a new bass (less than 2 years old) and especially on maple fingerboards. Dressing the fret ends may involve re-bevelling and re-rounding the fret ends, depending on how much trimming was required.
7. Play Test. This is the most important test the setup tech does. And it helps to have a lot of experience here. The tech will look for evidence of unevenness in the frets. A light dress of a problem fret or two should be part of the setup (or resetting of one or two loose frets). A complete fret dress is not usually considered part of a setup. The trick is in identifying if there is one or two problem frets or there is a problem with inadequate relief. Depends on the resonance characteristics of the bass, the type and gauge of string, the geometry of the fingerboard, etc. Yah, a lot of experience is an asset here.
And for what it's worth, a fret dress (even for a single fret) should consist of levelling, recrowning and polishing it.
8. Re-tweak everything - relief, string-height, intonation. The tech probably will not have to deal with the nut again, but sometimes it is necessary because of sympathetic vibrations behind the fretted note causing the string to rattle a bit against the lower frets. Damn fussy work to achieve a balance between easy playablity and freedom from unwanted noise.
9. Repeat steps 7 and 8 until it is right.
10. Measure and record everything. This part is optional, but better luthiers do this. But it's only worth doing if the tech is willing to spend the time with the player to learn how the player plays, his likes and dislikes,etc. But once you have the setup just right for a player, it's nice to have a record of the exact setup so you can reproduce it.
With experience, you might be able to do all of this in an hour - though it's not likely. On the other hand, if we're talking only about a quick truss rod adjustment, then an hour is too much time.
So in the case of a tech who's rate is $50 per hour, perhaps $100 for a setup is entirely reasonable. But if he is only setting the truss rod and string height, $100 seems pricey.
FWIW, I have seen advertised prices for setups that range from 37.50 to $200 (Canadian).
Best advice is to ask what you are getting for your money. And while you are at it, ask what the hourly rate is. And ask if you can get your instrument adjusted at no additional cost if it doesn't play right for you after the first setup attempt. Know what it is that you are paying for.
Then you can say if it's too much or not.