YnM is not really a yaoi series. It's shojo. They're both aimed at a predominantly female audience. Shojo titles are generally more mainstream than hardcore yaoi ones. There are some suggestive bits (more so in the manga) and the one rape scene, but that pales in comparison to yaoi titles. You can find out more about the terminology if you're interested on sites like Wikipedia.
As to yaoi being popular, well it's popular enough to get produced - as manga, dojinshi and animation. Overall, I would say that yaoi titles amount to a rather small fraction of the overall production on animation and manga but I say that only based on my own incomplete knowledge of what's produced.
Finally, as to feeling awkward watching it. Depends on what you mean by feeling awkward. I love YnM (both the manga and the anime). There are definitely parts of it that make me feel awkward - Muraki makes my skin crawl. Just my few cents.
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