Starting as early as the mid 1990s, according to the TV kid/adolescent sketch comedy show All That - as well as the 1997 film Good Burger - Americans were being strongly lobbied by a movement that insisted 'dude' is indeed gender neutral. The fact that they needed to be so explicit would seem to be evidence that they expected people to disagree - and indeed there were scenes and skits depicting characters who took issue with being called 'dude'.
There's even a song, entitled We're All Dudes! The chorus from the song insists:
I'm a dude
he's a dude
she's a dude
we're all dudes, hey!
The early late 1990s and early 2000s were a time of conservative social pushback, however, as evidenced by the film Dude, Where's My Car? where the term was largely reserved for males (both gay and straight). In the film The Big Lebowski (1998), The Dude was a male character - though notably male persons were not addressed as "dude", but rather as "man".
If you don't agree with this analysis, "Yeah, well, that's just, like, your opinion, man."
In American culture, at least, 'dude' has a history of being used to indicate - rightly or wrongly - uneducated, crude, or unrefined types (not merely surfers and skaters, but hippies and basically anyone who did not strongly associate with the "stiff shirt" upper-society and professional business types). It is not an accident that the media has portrayed characters using the word as idiots, and there is always an extent to which this bias both reflects and bleeds out into common society.
In summation: 'dude' is a word in flux, man. So don't, like, let it get to you dude. Like much of a common spoken language, they are terms that are often best avoided in formal settings where a more "proper" form of the language is expected. And be careful who you call buddy, pal, or friend, too.