For starters, they never had that really big blockbuster series. Konami, Capcom, EA......these companies have long lasting series that people identify with.
IReM doesn't have that. The closest thing they have is R-type which is relatively short lived as a series and doesn't get the genre appeal that some of the others get.
Don't get me wrong, I adore shmups. Easily my favorite arcade genre. But many people ignore them due to their diffculty. With the eye candy of recent years in the arcade and on the Sony and Sega systems, they're probably more popular now than ever before.
Secondly, it's because they are innovative. Innovation is popular in the underground, but the masses are spoonfed certain genre types to such an extent that while everyone is clamoring for innovation, sales for the copycats drive more copycats. This isn't exclusive to video games either. In fact, it's probably more prevalent in movies, TV, and music.