When someone looks at your company brochure or catalogue, they will almost always see the front cover first, then flick through it from front to back. Or after looking at the contents page, will jump to the section that they want.
Your website is different. Not all visitors will see your homepage first then click on the links to get to the section that they want.
Assuming that your website has more than one page, and assuming that those pages are all in the search engines, a visitor could enter your website at any page. The search engines will link directly to what they believe is the most appropriate page for visitor.
Other websites that link to you can also link to any page on your website, not just your homepage.
So what does this mean for you?
Well, if the search engines get it wrong and send visitors to the wrong page, you need to be able to direct them to the most appropriate place. Otherwise, they will hit the 'back' button and will try another website.
You must have suitable navigation on every page. Ideally, your main navigation menu should be identical across every page of your website to prevent causing confusion for you visitors.
Make sure that none of the pages on your website require the user to have visited another page beforehand in order for it to make sense. All pages should make sense on their own.
Have a quick skim through a selection of your webpages and make sure that thy are fully self contained. Make sure that, if they were the first page that someone saw, they would be able to understand what the website is about and easily be able to navigate to another page if they want.
If a visitor arrives at a page and doesn't immediately understand what it's about and how to get to where they want to be, they'll leave and choose a competitor.
You can't design a website so that the pages are in a specific order, there's is no order on the web, it's just loosely organised chaos really.