The Minutemen are probably the least "evil" morally speaking. But that's only from an organizational standpoint, because they aren't so much a faction with an ideology as they are an ad-hoc loosely organized volunteer militia. Individual minutemen, or even groups of them, are quite capable of doing 'evil' things. Such as is proved in Quincy and Libertalia.
The downsides of the Minutemen aren't really 'moral' though, its more logistics. The Minutemen are under-equipped local volunteers. Farmers who've probably never done an honest days military training their life.
They don't have much of a military organization to speak of. The General is basically just a figure-head. Someone they don't have to listen to and only nominally agree is 'in-charge' of this loose collection of independent fighters. They actually can, and will, blatantly disobey your orders (as in the case of T.S. Wallace).
So they lose points for that. You, as a player, have make the choice of whether or not the "goodness" of the Minutemen is worth them being far less equipped and disciplined than say The Brotherhood or The Institute. There's also no guarantee something like Quincy won't happen again. And just like that, they'd be right back where they started.