I disagree with this statement. The Starbucks CEO is using the "some of our customers are uncomfortable" excuse to politely request that a different subset of customers refrain from entering their stores (at least while carrying).
The analogy to segregation is sound - it emphasizes that one group of customers should be accommodated more highly than others, when the law doesn't provide a basis for denying accommodation. It is the nature of the request to surrender a right, rather than the specific right being surrendered, that makes the comparison apt.
What will be interesting is when the lack of "no guns" signs becomes an issue. And I predict that, in the face of a legal right to open carry inside a Starbucks, the lack of the prohibition signs WILL become an issue.