Disk performance causing SQL Server Command Timeout?
Command timeout simply means that your queries don't return in the 30 seconds allocated by default. What is the size of your database and how much RAM you have? 

The high disk usage is most likely a symptom, not a cause, and is caused by table scans, ie. missing indexes. A quick look at the execution plan of your timing out queries will reveal if this guess is correct or not (See Displaying Execution Plans by Using SQL Server Profiler Event Classes. 

As a general advice I suggest you approach this as a performance investigation and deploy the well tested Waits and Queues methodology.