Return default result for IN value regardless
Solution 1:
You have a condition on OnlineUseage the left join become like a inner join.
move your condition to the from clause will be better :
SELECT
users.Name,
users.ID,
IFNULL(SUM(users.Minutes), 0) AS MinutesOnline
FROM
users
LEFT JOIN OnlineUseage ON
OnlineUseage.ID = users.ID and
OnlineUseage.Date >= '2016-01-01 00:00:00' AND
OnlineUseage.Date <= '2016-12-31 23:59:59'
WHERE
users.ID IN (332,554,5764,11,556,.........)
GROUP BY
users.ID,users.Name
ORDER BY
users.ID