Yeah, apparently Tony purposely sped up and swerved towards him. That's certainly what it looks like in the video. Saying he was probably just trying to send a message and it was an accident is the exact opposite of assuming the worst in him.
Sprint guys (and all racers in fact) blip the throttle all the time under cation like that, although that definitely isn't a safe place to do it. The video is too tight for anyone to really know what went on except for the people who were there and Tony, all you can say for sure is that Stewart kicked his car out and it walked up the track into the guy who was walking down the track at him. Tragic for everyone involved.
And that quote isn't Stewart's it's his director of operations Greg Zipadelli's about the teams operations.
ZRod is correct. They just showed the press conference clip on ESPN. He (Greg Zipadelli) was definitely talking about the team. On a related note Regan Smith replaced Stewart in today's race.