I appear to be having the same issue as SergeiS & tonysonney under 14.04,
file system permissions are correct and cp works fine from the command line for one of my USB hard drives, but drive consistently shows as 'Owner: root' in Nautilus - even though mount options are identical to an automounted SATA drive that shows as 'Owner: me'

Other USB devices, (flash drive, HD from a different manufacturer) mount with correct Ownership in nautilus.. (also, i noticed everything that mounts correctly has a little icon in the media folder - a thumb-drive, internal disk icon, etc. while the badly behaving "root" media device does not have a little icon on the folder)

Ubuntu automount point permissions:
bjv@saucy10:/media/bjv$ ls -lt /media/bjv
total 16
drwx------ 1 bjv  bjv  4096 Nov 19 06:05 WD My Passport Ultra
drwx------ 1 bjv  bjv  8192 Nov 18 07:56 WD Caviar Black

Ubuntu automount options:
bjv@saucy10:/media/bjv$ mount | tail -n2
/dev/sdc1 on /media/bjv/WD My Passport Ultra type fuseblk (rw,nosuid,nodev,allow_other,default_permissions,blksize=4096)
/dev/sdb1 on /media/bjv/WD Caviar Black type fuseblk (rw,nosuid,nodev,allow_other,default_permissions,blksize=4096)

Dmesg:
[3345508.088038] usb 1-4: new high-speed USB device number 26 using ehci-pci
[3345508.269200] usb 1-4: New USB device found, idVendor=1058, idProduct=0820
[3345508.269206] usb 1-4: New USB device strings: Mfr=1, Product=2, SerialNumber=5
[3345508.269210] usb 1-4: Product: My Passport 0820
[3345508.269213] usb 1-4: Manufacturer: Western Digital
[3345508.269217] usb 1-4: SerialNumber: 575832314139344654415636
[3345508.269644] usb-storage 1-4:1.0: USB Mass Storage device detected
[3345508.270284] scsi18 : usb-storage 1-4:1.0
[3345509.268725] scsi 18:0:0:0: Direct-Access     WD       My Passport 0820 1012 PQ: 0 ANSI: 6
[3345509.269092] scsi 18:0:0:1: Enclosure         WD       SES Device       1012 PQ: 0 ANSI: 6
[3345509.269553] sd 18:0:0:0: Attached scsi generic sg2 type 0
[3345509.269840] scsi 18:0:0:1: Attached scsi generic sg3 type 13
[3345509.276843] sd 18:0:0:0: [sdc] Spinning up disk...
[3345510.280020] .ready
[3345515.207842] sd 18:0:0:0: [sdc] 3906963456 512-byte logical blocks: (2.00 TB/1.81 TiB)
[3345515.209831] sd 18:0:0:0: [sdc] Write Protect is off
[3345515.209837] sd 18:0:0:0: [sdc] Mode Sense: 47 00 10 08
[3345515.211210] sd 18:0:0:0: [sdc] No Caching mode page found
[3345515.211215] sd 18:0:0:0: [sdc] Assuming drive cache: write through
[3345515.216837] sd 18:0:0:0: [sdc] No Caching mode page found
[3345515.216845] sd 18:0:0:0: [sdc] Assuming drive cache: write through
[3345515.217232] ses 18:0:0:1: Attached Enclosure device
[3345515.226127]  sdc: sdc1
[3345515.229341] sd 18:0:0:0: [sdc] No Caching mode page found
[3345515.229352] sd 18:0:0:0: [sdc] Assuming drive cache: write through
[3345515.229356] sd 18:0:0:0: [sdc] Attached SCSI disk

Ubuntu version
bjv@saucy10:~/Downloads$ lsb_release -a
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 14.04.1 LTS
Release:	14.04
Codename:	trusty

bjv@saucy10:~/Downloads$ dpkg -l | grep 'nautilus[ ].*ubuntu'
ii  nautilus                                              1:3.10.1-0ubuntu9.3                                 amd64        file manager and graphical shell for GNOME

bjv@saucy10:/media/bjv$ getfacl /media/bjv/WD\ Caviar\ Black/
getfacl: Removing leading '/' from absolute path names
# file: media/bjv/WD Caviar Black/
# owner: bjv
# group: bjv
user::rwx
group::---
other::---

bjv@saucy10:/media/bjv$ getfacl /media/bjv/WD\ My\ Passport\ Ultra/
getfacl: Removing leading '/' from absolute path names
# file: media/bjv/WD My Passport Ultra/
# owner: bjv
# group: bjv
user::rwx
group::---
other::---