During the first third or so of BBS itself maybe, although even in their first meeting he didn't actually show much indication of fear.
Later on Ven's stance on Vanitas was obviously indifference i.e. on Destiny Islands "I'm through with you" (which is practically a more polite form to say "piss off") shows. Vanitas taunted him about being "too broken to talk back" but that was obviously from a time before Ven came to Eraqus where his heart was still damaged and he had no possibility at all to defend himself.
During the finale Ventus changed to annoyance and outright anger. Trying to kill Aqua was more or less the last straw that caused Ventus go into an uncompromising/unforgiving "now you're going down"-stance which remained right up to the final blow that destroyed the X-blade prototype.
Ventus explicitly wanting to destroy both the X-blade prototype and Vanitas himself may also shine some light on Ventus' stance towards him, which by that time certainly was no more "fear".
If some masked bloodthirsty sociopath started targeting me and everyone I cared about, I'd be pretty scared at first... Though like Sephy said, it seems like Ventus got over that by the end of the story, since the finale has him acting out of righteous anger.
The only thing he actually seems somewhat afraid of is when Vanitas says he'd choke the life out of Terra and Aqua. And that actually shows Ventus' character perfectly. It's always about his friends, isnt it? (At least he has some. Bla. I know. xD)