The reason it's so rare is because the songs are expensive to license, and they are also picky about it in general. When the film Dinner For Schmucks got the right to play the song "Fool on the Hill" in the movie, Paramount/Dreamworks paid $1.5 Million. (Yoko Ono & Paul McCartney also saw the movie first and enjoyed it.) For Mad Men, Lionsgate reportedly paid $250,000 to feature the song. Its not just the money though, because many have tried to get songs and have been turned down. They have to like the script & context of the song before signing off on it. Paul & Ringo are fans of the show, which helped. I believe this is the first time a Beatles song has been featured in a TV show, at least recently. A few movies have had Beatles songs in them though: Ferris Bueller's Day Off, The Social Network, Bowling For Columbine, & Nowhere Boy. Plus their own movies of course.
The cost is referenced in the episode itself as a joke. Early in the episode the characters are pitching an ad campaign with their concept playing off the Beatles film, "A Hard Day's Night." Their task is to find a song that sounds similar, since it is too difficult and expensive to get an actual Beatles song for an ad campaign. Its a little wink and nudge at the audience that AMC spent the big bucks to finally get a Beatles song in an episode. And it worked out perfectly, because the track fit in so well with the story and the time frame they are in right now. Don doesn't understand why music has become so important, because he grew up in the 1930s/1940s when it wasn't. There were no larger than life musicians. Halfway through listening to "Tomorrow Never Knows", after seeing clips of Peggy (Elisabeth Moss) smoking a joint while working and Megan laying down at her acting class with her mind "turned off, floating upstream", Don turns the song off and walks away. The generational differences are surfacing as Mad Men moves through the psychedelic era of the 1960s. Don is out of touch and can't understand the Beatles or the younger generation, yet he married into it. Pretty sure this marriage will end up on the rocks. What are the odds Megan becomes a member of the "flower power" movement?
And if you haven't listened to The Beatles masterpiece Revolver by now, go out and get it. Remember to "lay down all thought, surrender to the void" (unlike Don).