it actually goes through the center of the the two halves of the brain. Besides, if the humans are grown, then they can be genetically altered so that there is a hole created in the brain for a needle of that size to enter in. We really don't know the kind of technology that the machines are capable of, so we can't really dismiss anything without thinking of all possible alternatives, ie. genetic engineering. You have to remember that these aren't humans like us, humans that have been virtually genitically identical since creation. We do not know the anatomy of these humans. Maybe they are created without tonsils, maybe they have other organs, maybe they don't have a liver, whatever, we don't know how they are assembled; we do know that the needle can and does enter the brain, and allows them to be uploaded into the Matrix and Zion.
ok, have you watched the Animatrix, the second renaissance? the humans that were living were tortured. Ergo, they had to grow their own humans, much like we create our own batteries, or grow our own food.
It is also possible that the needle is exchanged for a larger one as the person grows up. we really don't know that much about the fields, so pretty much anything we may say is speculation, but it is possible that they can elongate the needles, or change them for longer ones. Who knows?