Income School LLC is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com. Income School LLC also participates in affiliate programs with Bluehost, Clickbank, CJ, ShareASale, and other sites. Income School LLC is compensated for referring traffic and business to these companies.
The concept of affiliate marketing on the Internet was conceived of, put into practice and patented by William J. Tobin, the founder of PC Flowers & Gifts. Launched on the Prodigy Network in 1989, PC Flowers & Gifts remained on the service until 1996. By 1993, PC Flowers & Gifts generated sales in excess of $6 million per year on the Prodigy service. In 1998, PC Flowers and Gifts developed the business model of paying a commission on sales to the Prodigy Network.[4][5]
first off, show visitors that you have a great site by getting a better theme! You did not get a penalty because of affiliate content, nor have I ever heard of, however, I have heard of sites in the past getting penalty for having do follow links to affiliate programs such as amazon, remember, google does not like you giving credit to a site in exchange for receiving paid compensation, so ask yourself, are your external links nofollow? this may also include any buttons/graphics that link to affiliate sites that do not have a no follow attribute, not going to go to much into this, so I am going to assume your content is ok, if it is, then you need to check your link portfolio; maybe you have too many low quality links and/or you may have over-optimized anchor/text in your link building efforts; bad links, over optimization are common link issues that could cause your site to get a penalty, as it is not about what you are writing about, if all else fails, then hire seo consultant for an entire site autdit, they will go through your site tooth and nail, and see why you have lost your rankings. good luck.
The people that you refer too did not master amazon, they merely mastered the value they offer to visitors. If you are able to engage/connect with visitors, then you got a winner, some people merely have better skills then others, which may include offering high value content, coding/custom skills. Do you agree that these people brought something to the table? If they did not, then visitors would not continue to visit their sites, right? You can put up all the content in the world, you can get all the backlinks you want, but if you can not engage/connect with your visitors, then all is lost. These site most likely did not start off with custom sites; they started off just like everyone else, some rag/tag site. I ran across an affiliate site a few months ago, and the content on his site would just blow your mind, and let me tell you,this guy had affiliate links from all major affiliate networks, his site has so much authority that he is listed right up under amazon, and some actual product manufacturers; how did he do this? He brought solutions, and value to his visitors, he knew what they were looking for, and knows how to engage, and connect with them. If you can not figure out how to blow your visitors mind, then what do you really have to offer? His avg reviews were between 7k-10k words? how about you? 500-1000 words? at the end of the day, which site will google find more impressive, yours, or his, and i assure you, he had far more affiliate links on his site then you have on yours as you could not skip-a-paragraph without seeing affiliate links. 
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