Notice there was only a male player until coincidentially Crystal.Now, I may just be making this up, but I think that the Pokemon franchise mainly caters (catered?) to young boys, which is why we have an overabundance of male looking Pokemon and a shortage (by comparison) of female looking ones.
Why is this important? Think of how the starters are associated. Most people picked Typlosion and associate it with Gold, leaving Feraligatr to Silver. Meganium is forgotten aside and then associated with Crystal.
Perhaps if diferent playable characters existed in R/B, Meganium wouldn't necesarially be the girly choice.
That said, I don't think it not being MANLY has really much to do outside of a loud minority. Pokémon nowadays is played mostly by people who are mature enough and by children. The only ones that would hold anything against it not being MANLY would be those that originally played gold and silver when kids.
Its problem though comes mainly from it not being particularly good in a competitive-obsessed fandom and having a horrible movepool indeed.
It is also a grass type, and people don't like grass types.
But I don't really want to talk about how people dislike Meganium. So I'll go back to how I like it and Venusaur.
In battling in general Venusaur does much better. But Venusaur wasn't always so good. Sure, better than Meganium still, but the gen. IV attack split did wonders for the thing. It's movepool is also very good and while I try to say Meganium is pretty versatile, it has nothing to do against Venusaur.
In design even, I'd say Venusaur is the better. Meganium's design isn't much when you look at it, but Venusaur's is really interesting both in apperance and concept. It is also the better evolution. (Though I like Ivysaur and Bayleef more)
... However I can't help it but preffer Meganium. I preffer the way it plays, having a supportive main character isn't exactly common.