"The padding issue isn't whether or not you're "man enough" to take the pain, it's a pure safety issue. #1: As has already been pointed out, with a pad you're more likely to have the bar slip off your back. Possibly hurting your or your spotter. (You do use a spotter, don't you?)"
No spotter except for the squat rack - I train alone. I've never had the bar slip yet, and hope it stays this way.
"#2: By adding the extra width to the bar you're forcing your head/neck forward into an unnatural position. When you start to go heavy this can and will cause damage to your neck. Also, with your head being forced forward like that, it doesn't allow you to maintain as upright a stance as you should when doing squats. This will force your weight onto your toes and can lead to severe knee damage. (On this I'm speaking from experience.)"
I use a squat bar that has a "U" shape that goes around the head so the big fat girly pad sits squarely on my traps and I hold the bar directly beside my shoulders. Hopefully this solves this problem.
"Do what's been suggested, build your traps/shoulder and develope a tollerance to the bar. You really do get used to it quickly."
If there are any issues with using the "U" shaped bar, please let me know, because otherwise it appears to solve the above problems making it unnecessary to get used to the unpadded bar on the traps.