I after upgrading OS X to Yosemite, rEFInd did not start. Using the Option key while rebooting, I selected my Ubuntu Trusty partition, which booted with a warning that the MacintoshHD couldn't be mounted.

During the upgrade, the HFS+ partition where OS X resides was converted to a logical volume of Apple Core Storage. I believe this is to support encryption, but I declined the option during the upgrade. The Disk Util app in OS X will not show this change, but the diskutil command will. The fix is trivial from the OS X terminal.

The diskutil list command will reveal which partition was convert to a logical volume on the physical disk.

diskutil list
/dev/disk0
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *251.0 GB   disk0
   1:                        EFI                         209.7 MB   disk0s1
   2:          Apple_CoreStorage                         175.6 GB   disk0s2
   3:                 Apple_Boot Recovery HD             650.0 MB   disk0s3
   4:       Microsoft Basic Data                         70.3 GB    disk0s4
   5:                 Linux Swap                         4.2 GB     disk0s5
/dev/disk1
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                  Apple_HFS Macintosh HD           *175.3 GB   disk1
                                 Logical Volume on disk0s2
                                 41AF7850-5594-4959-A135-582BF79FDE46
                                 Unencrypted

Your disk partitions for dual booting Ubuntu and OS X may be different. I know there was no logical volume before I started the upgrade. I restored the APPLE_HFS partition to the real disk0s2 with the revert option

diskutil corestorage revert /dev/disk1

When I rebooted, rEFInd presented me with choice of OS X and Ubuntu. Ubuntu mounted with MacintoshHD when I signed in. All fixed.