Something that had been tingling at the back of my head for a while:
Your CMB is adjusted by your size, however you also get all benefits of bonuses from other sources when using your CMB, that's fairly basic and easy to understand -- however here comes the loop:
A Goblin gets a +1 size bonus on attack rolls. He then gets a -1 special size modifier.
Now if we calculate CMB while including both the bonus and the penalty then they would wash out -- seems fair enough to me, you hit easier but due to smaller size you can't get the manuever off as easily.
However if we calculate CMB as it is presented in the stat blocks for many creatures not only do you take the penalty on the CMB but you don't get the bonus too. Now this doesn't follow mathematically or with pathfinder math since the bonus and penalty are for the same amount the penalty isn't "larger" and in real mathematics +1 is bigger than -1.
This gives a double jeopardy situation for small creatures and offers a double bonus to big creatures. The small one not only takes a penalty but also loses a bonus while the big creature not only gets a bonus but also loses a penalty.
This is also applies to CMD in an even more frustrating way since the size bonus to AC isn't allowed in either -- If the smaller creature is harder to hit in the first place he's still going to be harder to hit when you are attempting to do something specific to him -- and since all the maneuvers require contact to pull off that size bonus to AC should be relevant.
My basic thought is that the CMB/CMD adjustment for size should simply be something that "Washes out" the bonuses/penalties they take in the first place leaving them on even ground. Yes it can be harder to trip a larger thing -- but that larger thing is also easier to get to the right place to trip on, and several of the maneuvers also flat out stat you can't use them on something more than "x" sizes larger than you (generally x = 1) so that's already built in.
Thoughts?
In 3.5, a Large creature got a +4 to Grapple, Disarm, etc. checks due to size.
Now we're rolling those checks up into the Combat Maneuver checks, and he effectively gets a +2 instead, since his -1 is turned into a +1.
It's not that we're ignoring the fact that a Large creature is easier to hit; it's that we're saying that the total effect of the creature being Large on being able to do Combat Maneuvers on him is to make it slightly harder: a net +1, that is taking into account (implicitly) the normal -1 to AC but "overriding" it with his ability to shake off getting tripped, etc.
Some players actually put CMB and CMD "modifiers" next to their melee attack and touch AC statistics so that changes to those statistics can be easily translated when a Combat Maneuver is made; those "modifiers" include double the size mod. That may demonstrate more intuitively what's going on here.