FTM transgendered athletes are (generally) going to be taking testosterone.  However, their testosterone levels are monitored and have to remain within certain levels (which may well be lower than those of cisgendered competitors).  Nobody worries about the testosterone levels of other male competitors - the only concern is that they be "natural" and haven't been artificially boosted.  Fact is, trans athletes are held to stricter standards on that front than cis athletes.