Getting listed is free publicity for the company's staffing department and helps with morale, so if a company thinks they have a reasonably decent chance to make the list, and they're big enough to have data like this to hand, they submit to this. Only part of it is the HR/financial data submission -- Fortune also does random polling of employees, and in this case, Fortune actually sent a reporter to visit Hasbro and spend a day working at their factory, because they thought it was interesting. (I'm a HR consultant and I've worked on pulling data together for a submission before.)
The only downside to submitting but not making the top 100 is not getting listed. It's not like there's a list of shame or something.
I see ignoring some of the minor magazines that do similar awards, but ignoring Fortune would be silly if you have the resources and think you have a reasonable shot at making the list. I think several hundred companies try.