Charter flights chop and change on a regular basis according to customer demand. If an airline is struggling to fill seats, which in this case, it seems that Thomas Cook might have been, they may have acquired a percentage of the seats on another charter service. But by changing your airline, you must also accept the checked baggage allowance (and whatever other changes) offered by Monarch Airlines.
I am sure that you have a case, but most probably with Travel Republic. You entered into a contract at the time of booking and you paid a deposit to secure flights with one airline offering a 20kg baggage allowance. Now, through no choice of your own, you have had 5kg of this allowance taken away from you. I don't know where you are travelling to but the airline will charge you £5/kg for a short haul flight and £7/kg for a long haul. Whilst not a huge sum of money, that isn't the principle.
If Travel Republic, upon accepting your deposit, sold you seats on a specific Thomas Cook Airlines flight, then be persistent until you get what you want.
I have had a similar problem with British Airways. I travelled with them in January to the United States (which is where I am now). In a couple of weeks, I will return home to the UK. But between flights, British Airways changed their policy. Transatlantic passengers, until October 2009, could carry two suitcases at 23kg each. That allowance has now been halved and I was expected to accept this change and then pay £60 to take my second suitcase with me. Fortunately, with a copy of my original booking confirmation, the airline has accepted that I can carry the same weight home that I travelled out with.