It is not a new phenomenon that home pages are ranking quite low in comparison of certain niche pages. You must consider that search traffic for a specific local niche may rank much higher thank your website's general content. The flow of Google's web crawler may also not rank certain content due to their arbitrary algorithm, even if your website appears to be fully optimized for a human's eye.
Check Your Content
It should never be assumed that your content does not at least have a partial match of something else on the internet. If you are paying content writers to produce content for you, make sure that everything passes Copyscape or other plagiarism tests.
Special care also needs to be made with tags, meta descriptions, and titles. This is the first glimpse of what a user sees on your website to know if it is relevant to their interests. This is also what Google detects when they consider keyword relevancy.
If Google flags your content as duplicate, you better believe that it will not be featured towards the top. Too much duplicate content on your website, in general, may even lead to it being blacklisted.
Search Engine Algorithms Change
Google has a habit of releasing sneaky updates that completely blast the ratings of unsuspecting websites. Even websites that have followed highly trusted guides to a tee will be affected by these whimsical policy changes. The Panda update is notorious for affecting the ratings of many webmasters.
Make Sure Your Are Researching Correctly
During your SEO research sessions, using your own web browser is useless since Google will cater your searches towards your interests and search history. An even incognito mode may not be enough to anonymize your session so Google Adwords Keyword tools should be used for purity.
Once you take a look at the raw search data, you will get an idea where your homepage really ranks. Your search history may be affecting why some pages rank higher in your SERP than your main page. Your location and the location of potential users should also be considered when researching keywords.