JB,
Just like any shoe, a properly fitting steel toe should not rub. While they can be more difficult to fit you sould treat protective footwear like the gear we all spend hours selecting and trying out. There are a many different manufacturers of protective toe (steel, plastic, even kevlar) footwear and part of they reason they exist is the variation in foot shape and the variation in design of the toe box each manufacturer uses. If one type doesn't feel perfect try another make.
Another factor in fitting a protective toe boot/shoe is what socks you wear. I try to use Thorlow or Bridgedale socks so that I have a padded toe and top of foot in addition to the sole and heel. They also wick moisture well, keeping my feet drier. While they are expensive compared to a pair of gym socks I consider them to be gear also and part of what makes my work safer and more comfortable. (If I find I don't have a clean pair for the next day I can rinse them out with a little shampoo and they will hang dry in the bathroom by morning.)
If you use protective toe shoes/boots in your work you should also analyze the potential for dropping something hard and heavy on the top of your foot. If there is a frequent chance of doing this and it could break those small bones in the top of your foot I'd recommend a metatarsal guard. They can be had built in or as outside covers that lace into your boot/shoe. I just duct tape them in place when I need them.
My current favorite steel-toe is the Hi Tech steel toe boot. I find the toe box to have ample room to prevent rubbing, the boots are light in weight, they have good vibram soles that work well on soft and hard surfaces and they have good traction on floors. Oh, and you can find them on sale for under $40 sometimes.
Think I'm gonna get the sneakers someday!