However, when using GeoTrust/Symantec/Thawte certificates you can get a free SAN of domain.com if the Common Name of the SSL is www.domain.com, so the non-www version of the common name will be secured by the SSL for free.
SAN Example for COMODO PositiveSSL Multi-Domain:
CSR Slot #1: www.domain1.com
SAN Slot #2: domain1.com
SAN Slot #3: abc.domain1.com
SAN Slot #4: xyz.domain1.com
SAN Slot #5: www.domain2.com
SAN Slot #6: domain2.com
SAN Example for GEOTRUST True BusinessID:
CSR Slot #1: www.domain1.com
(as this is the main domain and www.domain1.com was specifiec inside CSR, domain1.com will automatically be included for GEOTRUST True BusinessID!)
SAN Slot #2: abc.domain1.com
SAN Slot #3: xyz.domain1.com
SAN Slot #4: www.domain2.com
SAN Slot #5: domain2.com