EWR is awful: winds the wrong way or a couple clouds, and it is cluster----.
As for the PD flight making it and the AC not, it can also do with altitude. Airways are more congested at FL300 levels vs FL200 levels.
A story to illustrate. I was flying COEX EWR»BUF in an ERJ145. We were stuck on the ground in EWR due to airway congestion. They refiled for a much lower altitude, burning much more fuel, to get us to BUF. Of course, this all took time to set up, so of course we were late, but we were 'home'. In talking to the First Officer upon landing, the reason they pushed it was so the plane was in BUF for the first flight out in the morning.
Basically, there are so many variables as to why you go, and the guy next to you doesn't (and vice versa), you are probably wrong when you guess why.
Brian