Figured it out. I ended up using the ComposedId property to map the Id column, which allows you to specify a IUserType for the Id column.
public class ExampleEntityMap : ClassMapping<ExampleEntity>
{
public ExampleEntityMap()
{
Table("Table");
ComposedId(i => i.Property(p => p.MyIdColumn, map =>
{
map.Column("MyIdColumn");
map.Type<MyIdColumnUserType>();
}));
Property(i => i.Country, map =>
{
map.Column("Country");
map.Type<CountryEnumUserType>();
});
}
}