Wood shim rot away over time.

Hard and soft plastic shims are made specifically for toilets. The soft ones are cut to lenght with a utility knife. The hard plastic shims are broken using a screw driver and hammer and using the screw driver as a small chisle. You could use a chisel, but the sharp edge of a chisel can easily chip or crack the new tile. A blunt screw driver is much less apt to do this damage. Besides, the shim is made to break-away with a sharp blow.

Any decent plumbing supply house will have the plastic shims for just a few cents each.

Hope this helps.