Actually, I say no. Although I could go either way on this, I think it might be somewhat easier for audiences to suspend their disbelief if she can't fly (that is, unless they're given a damn good explanation as to why she can-something which I don't think the comic books have done very well).
True, it's not like they really went into why Supes can fly in the movies and it still worked-but I've always found Wondy to be a powered down female Superman-with her physical powers at least slightly more plausible
There's precedence in the comic books for her not being able to fly. There is also precedence in the (like it or not) popular television show and Superfriends. These things would partly justify her flightlessness from a "canon" point of view. But I completely understand why someone would disagree with this since she's been flying in the comics for most of her appearances.
It just comes down to the fact that I don't think it's essential to the character that she be able to fly (unlike, say, with Superman).
Also, I speculate that the "invisible jet" is going to be some hi-tech, cloaked, military weapon essential to the plot. It won't really be hers, but she'll get to fly it at some point.