Starting from Lvl 9, a Monk using Flurry of Blows actually hits more easily than if not using Flurry of Blows. DnD 3.5 made using Flurry a trade-off... you got more attacks, but you gave up some hit-chance. At higher levels, the penalty went away. That just makes sense.
What PF 1e is doing doesn't make sense. Instead of the penalty just going away, a Monk actually starts to get a bonus to hit from 9th level on. What is the rationale for that?
Because the PF1 (chained) monk flurry is based on math rather than arbitrary bonuses at arbitrary levels.
Even though the monk is a 3/4 BAB class, when he flurries he is treated as if he is full BAB. (With a -2 penalty as if he is two-weapon fighting with light weapons and the appropriate feat.) That holds true at all levels.
If you’re asking “why did they make flurry of blows better than a regular full attack?” then the answer is “because flurry is assumed to be the default way a monk is going to attack whenever possible and we don’t want to penalize him for doing what he’s supposed to do.” That’s even more clear in the Unchained monk, which gets bonus attacks when flurrying starting at level 1 with no penalties.
you got more attacks, but you gave up some hit-chance. At higher levels, the penalty went away. That just makes sense.
No, it doesn't. You're treating it as normal because you're used to it, but there is no logic behind why the penalties are reduced at 5th and 9th level. Neither is it an even progresssion, unlike most things in the game, nor are those the levels other martials get notable things.
Also, most other classes get a bonus to hit, so for game balance it only makes sense Monk does, too. Fighter's Weapon Training scales, Barbarian gets higher bonuses for Rage, and so on. Rogue is the exception, but that class wasn't designed to be useful in combat, as people were still sniffing the "distinct party roles" glue back then.
For another point of view, it's only a "bonus to hit" compared to the Monk's medium BAB, but not to the baseline of a non-caster physical attacker with low skills, as that's full BAB. Paizo was too chicken to fix the mind-bogglingly stupid "those guys train all day long to archieve complete mastery over their body... but don't get full BAB and d8 HD" design turd WotC had layed, and this was a way of putting full BAB on the Monk without sacrificing the sacred cow.
Later on, when (more people at) Paizo began to understand balancing better, they not only gave the Monk full BAB, but also removed the -2 penalty for the Unchained Monk. Which is what everyone should use unless they want one of the few archetypes that drastically change cMonk (Sohei, Sensei, Zen Archer, Far Strike, Tetori).
Relevant rules text, with emphasis mine:
Starting at 1st level, a monk can make a flurry of blows as a full-attack action. When doing so, he may make one additional attack, taking a –2 penalty on all of his attack rolls, as if using the Two-Weapon Fighting feat. These attacks can be any combination of unarmed strikes and attacks with a monk special weapon (he does not need to use two weapons to utilize this ability). For the purpose of these attacks, the monk’s base attack bonus from his monk class levels is equal to his monk level.
Yes, it's clunky and not that obvious if you check out the table alone.
From a game mechanics point sheepishEidolon is correct. The chained monk is kind of a pseudo full BAB class. Meaning he is full BAB when using flurry of blows or combat maneuvers. 9th level is the point where his pseudo full BAB starts to overcome the -2 penalty.
If you want some in game justification around that level is when the monk starts getting a lot more attacks, so his blows are becoming a lot faster so are harder to avoid. They actually start getting more attacks than normal at 8th level, but it is fairly close.