How do you stop tradesmen from doing whatever they want?

I guess you could have told him that regardless of what he thought the problem was, you wanted a new toilet, that you did not want the drains looked at or cleared. One of the things you pay tradesmen for is their experience and advice and ability to diagnose what a problem is. Lots of times, anyone could fix a problem if they could only diagnose what the problem is. It would be a little clearer if you had said what exactly you mean by a weak flush--was the toilet not flushing what it was supposed to flush, was it backing up, or what? In any case, it can be very hard to establish what is causing a problem until you try one of the solutions. The plumber did in fact do the work you were charged for and it might have been a very good thing to have those tree roots removed. I don't see that you have a case for stopping the cheque. Plumbers are usually busy enough with legitimate work that they don't need to go around inventing it.