The Wonder Woman animated movie failed for quite a few reasons.
For starters, she isn't Batman or Superman. Both Superman and Batman are widely popular and well known, having had numerous animated TV shows, video games, recent liveaction TV shows and movies. To be frank the concept of a DC trinity is a joke, being more like the DC duo.
Then there's Wonder Womans outfit, which at best looks like she's wearing a swimsuit to a 1960's playboy swimsuit competition. When they deigned to give her pants and make her look a bit more up to date, comic fans foamed at the mouth.
Speaking of male comic fandom, lets face it not a small proportion of them have issues seeing ladies as anything other then sex objects (but then same goes for geeks/nerds), some even being openly misogynistic. Not all of them, probably not even close to a quarter of them, but enough. At least that's my feeling based on comments I've read on comic websites.
Finally there's the concept of the character herself which seems to take two forms. Domination fantasies of strong women dominating men (and in some cases men dominating strong women) and a very bad parody of a straw feminist. The character herself is uninteresting and bland to the point of making Superman look exciting as a character. Batgirl, Zatanna, Barbara Gordon as Oracle (heck she'd make a better member of the trinity then Wonder Woman) and Supergirl would have been better stars of their own movies.
Basically the animated movie was doomed to fail from the very beginning.
Regarding superheroine movies as a whole, I suspect a large portion of the problem comes down to how they're written and designed. With a female superheroine they tend to go overboard in one way or the other, whether that's sticking her in a stipperific outfit and/or feeling like they have to make a feminist statement with it. Not that there's anything wrong with that, just that they do whack it over your head with a blunt instrument in a way Buffy didn't. Also there's a lack of focus on the character herself, unlike in superhero movies (especially recent ones) that focus on the characters inner turmoil and problems etc.