Ok, myślę że coś takiego:
<!DOCTYPE html>
<html lang="pl">
<head>
<title></title>
<meta charset="utf-8">
<style>
</style>
</head>
<body>
<input id="master" type="checkbox" /> Master CheckBox :)<hr />
<table>
<tbody>
<tr style="display: none;">
<td><input type="checkbox" /> 1</td>
</tr>
<tr style="display: none;">
<td><input type=" checkbox" /> 2</td>
</tr>
<tr style="display: none;">
<td><input type="checkbox" /> 3</td>
</tr>
<tr>
<td><input type="checkbox" /> 4</td>
</tr>
<tr style="display: none;">
<td><input type="checkbox" /> 5</td>
</tr>
<tr>
<td><input type="checkbox" /> 6</td>
</tr>
<tr style="display: none;">
<td><input type="checkbox" /> 7</td>
</tr>
</tbody>
</table>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.1.1/jquery.min.js"></script>
<script>
$(document).on('click', '#master', function() {
var masterStatus = $('#master').is(":checked");
$('tr').each(function(index, element) {
if($(this).css('display') == 'table-row') {
$(this).find('input').prop('checked', masterStatus);
}
});
});
</script>
</body>
</html>