Counting the number of recordings on sale at Amazon seems like a reasonable metric of marketplace popularity, although at the Mozart v. Beethoven battle of the titans level, Mozart probably has an advantage because he wrote more music than Beethoven (e.g., 41 symphonies v. 9). If you are an obscure musician, you might try to pick up a few bucks from Mozart completists by recording an obscure Mozart piece. So, number of recordings on sale doesn't necessarily match up to sales. But, it seems likely to be good enough.
As you can see, overall, scholars and classical CD-buyers don't disagree all that much. Still, the scholars value early composers (pre-Vivaldi) more than the public.
The other main area of disagreement is over 20th Century composers, especially atonal ones such as Schoenberg, Webern and Berg. (If you are not familiar with the music of Arnold, Anton, and Alban, this KTEL-like 1977 infomercial for a greatest hits album entitled "Beloved Hits of Arnie Schoenberg and the Second Viennese School" will get you up to speed.) They were very talented at impressing scholars with the idea that they were the Next Big Thing in the History of Music, but the public has been less impressed.
The only two major composers from the second quarter of the 20th Century to be more popular with the public than with the scholars are Prokofiev and Shostakovitch, both of whom had to worry that if they let their compositions get too avant-garde, the middle-brow (but highly opinionated) Stalin would have them shot. So, the classical music-buying public evidently owes Stalin a debt of gratitude.
The composers who are most popular with the public relative to their importance to music historians tend to be the Romantics from the second half of the 19th Century. The scholars rate opera composer Giacomo Puccini (Madame Butterfly) only 10% as important as Mozart, but Amazon carries 30% as many Puccini titles as Mozart titles. (Puccini's aria "Nessun Dorma" from Turandot has become a staple of television talent shows in the last few years.) Next in line is Bizet (Carmen), then Tchaikovsky (The Nutcracker), and Dvorak (The New World Symphony).
Then comes the early 18th Century Baroque composer Vivaldi (The Four Seasons). It's possible that the scholars are underrating Vivaldi's importance in music history because most of his compositions were lost from the late 18th Century until the 1920s. However, he was known to J.S. Bach, and had some influence on him.
Others more popular than their degree of scholarly eminence would suggest include Grieg, Verdi, Gounod, Saint-Saens, and Brahms (although, obviously, Verdi and Brahms are giants by any measure).
I wonder if opera fans are more likely to buy multiple versions of an opera than are symphony fans, which might account for opera composers doing well in terms of number of recordings on sale. To my untrained ear, it's easier to be a fan of a particular singer than a particular conductor or orchestras, so there might be more demand for multiple versions of operas.
At the other end of the scale—composers more written about than played—we find, besides a lot of early composers and the late 12-tone boys, Cherubini. I had never heard of Cherubini, but Beethoven saw him as his greatest contemporary. Other big names on the Important-but-not-Popular list include Stravinsky, Berlioz, Weber, and Wagner.
Murray's methodology might overrate Berlioz's representation in music reference books because one of Murray's techniques is to look at the index and count the number of pages a composer's name appears on. Berlioz was not only a great composer (Symphonie Fantastique), but also a great music journalist. So, he gets quoted a lot about other people, which inflates the number of times his name appears in indexes relative to a composer who let his music do all the talking for him.
Evidently, the craft of composition had reached maturity in the second half of the 19th Century. By then, most of the tools to appeal to the music-literate public had been created. Strikingly, the composer universally believed by musicians to be the greatest genius of the second half of the 19th Century, Wagner, is not particularly popular these days compared to the awe with which he was regarded a century ago. After about 1900, however, the enormous richness of the 19th Century repertoire weighed down composers, driving them into experimentation, most of which has not proven enduringly popular with the CD-buying public. Wagner got there first, and was able to create popular interest in his innovations that lasted for a few generations, but without him around to blow his own horn, public appreciation for Wagner seems to be fading relative to his Italian and Viennese rivals.