The limit is controlled by the TD. It can be set anywhere from 0% to 100%.
"The timeout % is hidden from prospective registrants. If it is different from the default 10% a TD should include this in the description."
It is often not in the description.
http://www.chess.com/groups/forumview/9---max-timeout
Edit 10% default not 5%.
According to my stats, over the last 90 days my total 'Timeouts' has been a miserly 2%. by anyones reckoning that's very, very low and yet i've been refused entry from a few tournaments because it's deemed too high!!
How low do i have to go before i'm eligible for some tournis....? ... 1% ?... 0.5% ?...or maybe........ -1% ?