Long gone are the days of a single entry point and a controlled funnel for users to experience your site. Now, every page of your site needs to work as a first impression while responding clearly to the request that got them there in the first place.
The dynamic of search and email have forever changed our ability to "control" our user experience. I think this is a positive thing. Instead of being in the business of guessing, we are now in the business of responding. Basically, it would be like going to a restaurant and being served a meal you didn't ask for and the chef hoping he got it right.
Now you can order.
This does come with challenges, however. If we stick with the restaurant analogy, you still need them to like what you serve and provide more than they asked for so they will come back. In the world of websites and homepages, we see more traffic off the homepage then on. Since people search for what they want, if you have it, they will go there.
What to do? Forget the top-down model for starters. Think about every page on your site as a potential destination. What do you want to say? You can simply answer the request with your content. That's a start, but it won't build from there. Carefully assess your ability to communicate and your potential messages. In other words, if someone searched and found your page on shoes, maybe you should tell them 1) you make the best shoes 2) you have a lot of shoes and 3) you have more than shoes and would you care to take a look?
Lastly, you have a homepage. Just because people spend less time on it or find you through other means does not mean you don't need to have one or should ignore the opportunity it presents. As you think about making your whole site work harder for you -- to go from here it is, to here is more -- you should also ask yourself what your homepage should say to the world. Often it says way too much. Just when you thought you could throw everything at someone and hook them, you discover you said nothing and they didn't get it. Find a couple of things, products, messages, whatever, to say to someone and say just that. For example, my company's 'divine caroline' homepage says, "I'm a site for women to come share their lives in their words across many topics, here they are…"
Look at your homepage. What does it say to you?
Don't worry about being perfect. Just get better. We are all in the digital world because we love change, aren't we?