Well, do the math for uptime. 99% uptime means that about every 3-months, the server can go down for one entire day. Now add on that great extra .9% that Hostony puts on there.
There is still a margin of error, and sometimes the problems may be very complex, and might be related to hardware or something else.
As far as Matthew's problem... I dont know any details.
If the domains are down, than its the domain registrar's fault. If your server is down, its a whole nother thing.
Details please. Please provide a domain or something, so us forum members can try to help.