Well sometimes you can find the fresh air intakes and what have you and put hardware cloth over them that will help some(at least keep them out of the air filter.No this is not peculiar to Toyotas,even Briggs and Stratton engines should have the blower shroud and sheetmetal removed every spring and the rats nests cleaned out.
Glue boards traps will help,but the rural setting almost guarantees rodent problems-Kevin