A nega is only tamei if a white hair grows in an already existing baheres -- "se'ar lavan ba'baheres" -- but if the white hair grows first and then the baheres develops around it the nega is tahor. Where there is a safeik as to which developed first, the white hair or the baheres, the braysa (Kesubos 75b) tells us that the Tana Kama rules the nega is tamei and R' Yehoshua ruled tahor. What is the reasoning behind the Tana Kama's view in this case? Every person has a chezkas tahor until proven otherwise, so why, absent incontrovertible evidence to the contrary, should we declare a person tamei just because of a safeik alone?
Rabeinu Tam explains that the case being debated must be where there is already an existing nega on the person's body -- the person had a chezkas tumah, not a chezkas taharah, when this additional nega developed. R' Yehoshua nonetheless declared the person tahor because counterbalancing the chezkas tumah is a chezkas haguf, a physical chazakah that the body is free of nega'im until proven otherwise. The debate between the Tanaim boils down to which chazakah carries more weight: the legal chazakah status of tumah or the physical chezkas haguf status of purity.
The obvious difficulty with Rabeinu Tam's view is that it requires assuming that the braysa is addressing only a very specific scenario and leaves us to deduce the details. The Rash (Negaim ch 4) therefore explains that the Tana Kama disagrees because in most cases the baheres done indeed precede the emergence of the white hair. Tosfos (Nida 19a) presents a simialr view that we are dealing with a lopsided safeik because usually white hairs emerge from the baheres and not vica versa.
The common denominator between Rabeinu Tam and the Rash is that they assume the Tana Kama held that the nega in question is definitively tamei. The Rambam (Tumas Tzara'as 2:9) interestingly writes "v'yireh li she'tumaso safeik". Yes, the nega is tamei, but not because we resolved our doubts, but rather because when in doubt, be strict. Apparently the Rambam must have held that the fact that the baheres usually precedes white hairs is not an absolute rov -- it provides only enough weight against our chezkas haguf and chezkah taharah to call this a 50-50 safeik (Chazon Ish Negaim 5:20. This issue is addressed by numerous other Achronim as well.)