I use datatables as well. Love it but dont use the added classes for 'zebra stripes' lol.
If your users are past IE8 you could just let CSS do it like so:
tr:nth-child(even) {
background-color: #000000;
}
EDIT: Based on comment. If you will be hiding rows rather than removing them jQuery is the best answer. Note the ":visible" in the selector. Using addClass would be a better call hence we could removeClass from the tr selector before we stripe the table.
Or use jQuery:
$(document).ready(function()
{
$("tr:visible:even").css("background-color", "#000000");
});