Go-Ahead (who own 65% of Go-Via, which operates the London Midland, Southern and Southeastern franchises) reported £40M operating profit for rail in 2012, with a margin of 2.3%.
FirstGroup (who operate three franchises, co-own another and have one open access operation) reported £63.2M operating profit for rail in 2012.
Stagecoach Group (who operate two franchises and co-own another [*] and have one tram operation) reported £49.9M operating profit for rail & tram in 2012/2013, with a margin of 4.2%.
Virgin Rail Group (who operate one franchise and are co-owned by Stagecoach) reported £12.8M operating profit in 2012/2013, with a margin of 2.9%.
Obviously, with the exception of VWC, that's not broken down per franchise - but overall the big groups are all in profit on their TOCs.
[*]I'm not sure if these figures include Stagecoach's share of VWC or not.