Aquaporins exclude passage of hydronium ions (h3o+), but some aquaporins allow passage of glycerol, a three-carbon alcohol, as well as h2o. since h3o+ is closer in size to water than glycerol is, yet cannot pass through, what might be the basis of this selectivity?

The maintenance of electrochemical potentials can be disturbed if protons freely pass through the membrane protein. Aquaporins are proteins that form a channel to allow passage of water molecules and some uncharged molecules as glycerol, but not of hydronium ions.  The way aquaporins exclude the entry of protons (H3O+), seems to be determined by the amino acid composition of the implicated polypeptide chains, and also dipoles.

Explanation:

Aquaporins forming a tetramere, for example AQP-1, is known.  Its monomers, consisting of 6 transmembrane helical segments and 2 short helices, each containing the sequence Asn-Pro-Ala (NPA), forming transmembrane pores.  NPA are hydrophobic amino acids.  

Crucial residues of Arg and His, and electric dipoles occurring in the short helices of NPA loops supply positive charges in positions that reject a possible protons pass through the pore.   Particularly, charged positive ions (as histidine, arginine, or lysine) in certain sections of the aquaporins, repel those H3O+, as they share  similar charges.