Most people look at the monk and expect it to be what it was in the Advanced D&D days - a hideously powerful combat focused class. PF did not underpower the monk, they changed what the monk was. For what it is, it is pretty much built just right for their own system.
I've been playing and running PF for quite a while, and I figured out how they balanced combat.
3.5 casters pretty much ended all combats of their CR in one or two rounds. three if they're unlucky. Rather than simply remove all the broken spells, they modified them to work at that power level only if the caster was focused on that type of magic and spell. Then they pushed the full melee classes to that same level of capability - all the full melee classes can slaughter anythign of their CR in one or two rounds, three if they're unlucky. Then they took the 3/4 BAB non-full casters (rogues, bards, and monks), and gave them more utility out of combat compared to the other two sets of classes (because even with spells a caster is no match for a skilled class at what that skilled class does), while making them weaker in direct combat....UNLESS they are directly helping another 3/4 non-full caster or backing up a full melee or full caster. If you use 3/4 non-full casters together, say magus and monk, rogue and inquisitor, summoner and alchemist, etc., you are both combat capable and also more versatile than say, a Full caster and a melee class, or two full melee, or two full casters.
Then they pulled another trick, and made CR actually matter. CR=character level-character level wealth. If you give a monster character level wealth, you have to add 2 to it's CR. Then they made sure that anything over CR 10 either had a batch of immunities, or was the equivalent of a prestige classed, multiclassed character. Fae are like Mystic Theurges, two spellcasting classes in one with their racial magic combined with magic. Aberrations tend to fall into a similar category, with more debuffing plus full casting than double spellcasting. Outsiders are Eldritch Knight material, while dragons are Eldrtich Knights dialed up to about 13.
But, back to monks. Monks are not full combat characters - they're 3/4 BAB characters. With the abilities they have basically, they're designed to get anywhere, avoid getting removed from combat by damage, spell, poison, power, or any other ability that would ordinarily remove a character from combat, and get whatever they need to do done. They can fight really well, if they get a full attack action, but really, their strength lies in versatility and mobility, rather than lethality. their stunning fist combined with vital strike can cause lots of trouble, while their sheer movement abilities can make them part of the battlefield itself, gettign wherever they must be no matter what its in their way (to save someone who is about to die, to back up the rogue with a much needed flank, to stun a caster into insensibility to help out the party for a round so they can get into better positions, etc.). Everyone is used to monks being the AD&D combat monsters they used to be, and they simply aren't that anymore.