Compressing matter in to a black hole does not increase it's gravitational pull overall. If the sun were to suddenly compress into a black hole, Earth's orbit would continue undisturbed.You're right of course. Brian was saying that there are greater energies in our upper atmosphere than the LHC can yield- so nothing new to worry about.
Likewise, if you were to compress a coffee cup into a black hole, your orbit around it would continue unabated.
If we compress some subatomic particles into black holes, other atoms would continue to orbit around them as normal. Only if something were to come in contact with the black hole "horizon" directly would anything change. Given the size of the black holes generated by the LHC and in the upper atmosphere, the likelihood is they could pass between a hydrogen electron and nucleus without disturbing anything.
So, I don't see much to worry about.