I feel like the question "Do bronies challenge traditional masculine values?" is running under the assumption that a "normal" male would ONLY engage in traditional "male" activities. What are things involved in masculinity? A desire of physical and sexual dominance? Placing significant value on physical strength and virility? Having a knowledge of mechanical tools and devices?
And then, because it's just as important to this question, what are traditional feminine values? Fine motor skills (being able to thread a needle, sewing small stitches consistently, etc)? Placing significant value on sexuality and seductiveness? Placing significant value on taking on and completing domestic tasks (raising kids, cleaning the house, etc)?
I think to say that "normal" men NEVER engage in feminine activities and "normal" women NEVER engage in masculine activities is silly. I know my boyfriend does dishes at his apartment and cooks food, and I like to exercise and I know how to hang drywall. So in order to be a functional and independent human being, there needs to be a bit of overlap on the part of both genders.
And everything else there that isn't a task is something either the person takes on themselves or is a part of their personality. Yes a stereotypical male trait is a desire for sexual dominance, but that isn't always the case. In fact, in my experience guys who place too much value here tend to be manipulative jerkwads who end up in prison at some point. Physical strength? Well yes some men are "born with it" more and you can build yourself up if you aren't, but working out is a lifestyle choice and not all men do it, and most of society doesn't care if a guy works out. Well yes if he weighs 700 pounds there might be some judgment, but you don't have to be totally ripped just to get by. And the same is on the female side: you choose to have kids, choose to do things like sew and knit, and sexuality and how much they put on display depends on their desire for such attention and level of extroversion.
Now of all those things, I can't really spot one among the male camp that would prohibit the enjoyment of something like My Little Pony. The thing that is most feminine about it is the art style. Otherwise, MLP is sort of a masculine show, really. Ponies with superpowers that fight evil and mischief when it comes knocking, standing up for their friends, defending their homeland, helping each other grow stronger as people (er, ponies).
Yes men aren't the target demographic, but the target demographic of the Ninja Turtles and Transformers wasn't girls and the shows weren't feminine at all yet nobody raises an eyebrow at girls who love them. Perhaps grown women, but I think it's generally known at this point that even adults can love cartoons.
So, yeah. I think the reason so many have flipped their shit over men liking this when nobody really did so when the PowerPuff Girls was big is because MLP is more overtly feminine in the art style, and the age of the men is a little up there. And I think the explanation for that is simply because the show is structured like a cartoon from the 90s. A regular cast of characters all with their own personalities and flaws, overcoming life and other obstacles while learning valuable moral lessons along the way. And who grew up in the 90s? Why the 20 and 30-somethings of today. So it stands to reason a show of that format would catch the attention of that generation. It would be like if a flawless reboot of the Flintstones was launched. The 60s and 70s kids would be all over that show.