I didn't say he had a problem with the mods, there's evidence of the opposite in the fact they're making the API and he's said he doesn't mind them before. There's a bit of a grey area with inserting to code into a legit .jar, it's still decompiling his code and such, but definitely not flat out illegal like redistribution. I believe he's also said he doesn't like the hacking, but that he's not going to go after the modders in the past. Not being able support it doesn't mean he's actively against it.
Still, he can't go about helping the modders right now as he can't support hacking of his product. It's akin to Honda telling people how to install a NOS system on their cars or offering help installing it, it's just not going to happen.
And yeah, loads of servers use CraftBukkit and that makes patch days suck. I've got no idea what a vanilla server offers in the way of management tools against CraftBukkit as I've never needed to work on that side of things, but I assume that the vanilla tools leave a lot to be desired in comparison. API will fix it, once that's in place I would assume that Notch would be able to open a dialog with the CraftBukkit guys to help get them the tools they need into the API.
Also, I don't see how you can say he's got little regard for modders when he's actively working on the API that is for modders to use to make mods to run in his game. An API is a massive boost to the ability for mods to run, be created, and be stable between updates. It's what the games NEEDS if you want mods to be extend the life of the game. There was the password steeling mode a little while back; that can't happen with the API. You really need to trust the source of the mod right now, it's easy to have them execute arbitrary code on your system, API solves that problem.
Currently these mods work by changing the games code directly, and each patch changes the code. You can't work with a ball of chain keeping you from changing the code the modders use, it's just not possible. He's not breaking them on purpose, it just happens when he's doing his job of developing his game. Once you've got the supported API there, you'll be calling commands from that which will already be updated to run.
It's really all boils doing to the API. He's working on it, once it's here everything will be good and everyone can be happy.