Lunch time is an opportunity to socialize with your colleagues. It's also a great time for spontaneous collaboration to take place. I've worked at a startup where great ideas were born out of engineers, operations managers, and customer service reps eating sandwiches together. It's cross-pollination that does good for everyone.
A lot of companies also combine lunch with talks, presentations, or team building activities. In general, I care deeply about working with people that I look forward to chatting with during the day.
If you can imagine a place where most people eat alone at their desks, what else might this signal? Maybe people aren't friendly? Maybe everyone is expected to work through lunch? Maybe people are very exclusive and leave the office in group without inviting "outsiders"?
The worst teams I worked in expected a lot unofficially-mandatory socialization where your status and work progress depended a lot on your ability to be charming and fun. Did not prevented bad politics.
It's an easy proxy to see that your team mesh well together (if my "best friends" at work are also my team members, chances are we'll work well together). Plus we'll end up discussing work problems we all have and that lunch time can turn into solutions.