I'm fairly positive Wish You Were Here is more popular with the general public. Based on personal experience, most people who are not familiar with a lot of the band's catalogue will at least be able to list Wish You Were Here as one of their favourites. At the two Roger Waters shows I saw, the whole arena would sing along with WYWH. A lot less sang along to SOYCD. The only people I know who would consider SOYCD a favourite are more familiar with the band's work/rock music in general (i.e. not the type of people who'll only listen to the radio and leave it at that), or they're hardcore fans.
The reason why we think SOYCD should be winning the contest has nothing to do with popularity, but more with the curious pattern to the voting. It is, of course, entirely possible that people are genuinely voting SOYCD off in favour of WYWH. However, the sudden onslaught of votes just doesn't seem to compute. Especially given that the voting has been fairly sluggish up until this point. Money is one of Pink Floyd's most popular songs (more popular than WYWH, I'd be willing to bet), and it didn't win the DSOTM contest. Therefore, there's no reason to think that WYWH would naturally win because it's more popular than SOYCD is.