What's with the flying, anyway? Where was He going? We know that Heaven isn't simply up, up, and away. Jesus had been content with suddenly appearing out of thin air before; He didn't fly in through a window when He first came to see His disciples after His resurrection. For that matter, He had even chastised the devil before for trying to convince Him to jump off a cliff since the angels would catch Him anyway.
I really don't have the answers to this confusion on my part. I suppose that appearing to people who tried to have you killed the first time might be pushing things a little. For that matter, who's to say that He didn't and that they refused to believe that they weren't dreaming, or that they dared not to tell anyone out of fear of being called crazy. "You know that guy I had nailed to a cross last Friday? Yeah, well, he stopped by the other day and asked for some fish ..."
As for the flying, it's not the first time that one of God's chosen had been lifted into the sky. If it was good enough for Elijah ... Also, the angels who appear to the disciples immediately after Jesus takes off tell them that He would return in the same manner. Perhaps it is a way for us to recognize Jesus once He returns. This way, people who falsely claim to be Jesus can be put to that simple test. "Yeah, weren't you supposed to fly in here?"
I know I'm being a bit flip this Sunday, but it's these readings that gave me so much trouble when I was younger. For a long while, I was willing to believe in God, but I refused to believe in Jesus. I felt that questions like I listed above weren't adequately answered. I didn't understand why Jesus wouldn't have done something more substantial to prove that He had risen from the dead. As is, it was too easy for me to believe that His disciples simply stole His body and hid it, later writing down a false trail in order to keep people believing them.
I'd like to say that I have no doubts since then, that I found a magical answer or had a miraculous vision (oh, how I want one of those) since then that answered all of my questions and calmed all of my fears. I haven't. Instead, self-examination has shown me that Jesus, even if He wasn't divine, had the right answers. There's nothing about what He said or taught that isn't True (note the capital "T"). If He's right about those other things, then I should also trust Him when He said He was divine and destined to die and rise for our sins. There are enough other perfect flaws (rising on the third day only meant a day and a half in the tomb) that suggest to me a level of interconnection that His original disciples would not be capable of putting together.
I believe in Jesus despite my doubts.