Sometimes there may be a difference in the type of standard rooms that each company uses which can make a difference to the price that that the operator charges, for example Thomson might have a sea view room as their lead in standard room while TC might have an inland or limited view as their lead in room.
It is very much swings and roundabouts, one is cheaper for one holiday and the other is cheaper for a different holiday that is why it is important to shop around, we just booked on Friday to go to Kenya next year and the identical date ,hotel flights etc was £700 cheaper with Thomson than Thomas Cook
We haven't holidayed before with Thomas Cook so are edgy ---- like I said, too good to be true !
I wouldn't worry about going with Thomas Cook, apart from one problem just after they took over Direct Holidays who we had booked through we have not had a problem and have used them many times, just as good as Thomsons
Graham