One reason these are rare: if a bootstrapped company is valued at $100+ million, a small minority investment - say, 10% - is very meaningful cash for the company yet involves relatively little dilution and little or no loss of control. It gets a lot harder to justify not raising something.
(And yes, a bootstrapped business worth over $100MM is probably generating a meaningful profit, but the founders may not be comfortable reinvesting it.)
It also helps build relationships and align incentives with powerful firms that can be very useful in arranging an exit and getting the best price for it.
Microsoft took a small mezzanine round right before they went public. They didn't need the cash, but it brought investment bankers on board so that they had an incentive to get the best possible price in the IPO. Similar story with Whatsapp; they didn't need the cash, but having Sequoia on board gave them a stamp of approval that probably helped their negotiating leverage both in attracting employees and in selling to Facebook.
(And yes, a bootstrapped business worth over $100MM is probably generating a meaningful profit, but the founders may not be comfortable reinvesting it.)