Bookexp:
I work for a large company in the EWR area. We guarantee CO a large amount of business ($$$) per year. Based on that they give the company a certain discount % (upwards of 20 %)on certain (most) routes. As part of this deal they give employees of those firms (AT&T, Lucent, Johnson & Johnson, etc.) access to the special check-in line that you mention that is open a good part of the day.
There is no policy that employees of those companies get comped to elite status or get any perks (besides the short check-in line)