Well, the short answer is ads, subscriptions and off the rack sales; in that order in terms of lucrativeness.
There are those who may contend that free magazines are 100% ad revenue based. Of course, there could be nothing further from the truth! We all pay a little more for convenience, i.e. milk at a 7-11 or similar convenience store is priced more than at most supermarkets. Readers will subscribe to free magazines for the convenience of having them delivered directly to their residence as opposed to having to look for them, and possibly miss an issue, at public points of distribution. For free circulated magazines, ads and subscriptions are the primary revenue stream. For paid publications, of course, there is also off the rack sales but this is considerably less for most publications unless the magazine has an extremely large circulation and an excellent sale through ratio (the actual percentage of magazines sold, out of the total amount distributed, per issue per retail location). Another revenue base that both types of magazines can capitalize on, and has yet to be mentioned by previous posters, is merchandising. With the advent of commerce ready websites, it's easier now than ever before to sell merchandise related to a magazine's brand.
It is also possible to garner a significant consumer base, not only predicated upon the magazine's core demographic but also via social media sites with very little or no investment. If a well thought out marketing plan is properly planned and executed, the merchandising realm can certainly be much more lucrative than the aforementioned options!