Hi Dazed,
I can imagine how frustrating that must be. If it makes you feel better it even happens to Super Affiliates sometimes. Check out this blog from Super Affiliate Zac Johnson:
Where Did All The Good Affiliate Programs Go?
Declines happen for a variety of reasons and each merchant/affiliate manager has different criteria.
1) Some affiliate managers and merchants are just plain clueless and don't know how to review and select affiliates.
2) Many screen out affiliates if their site does not match the merchant's product category. Example: affiliate applies to a baby stroller affiliate program with a golf site. Narrow minded AMs decline. Sharp AMs realize that the affiliate is probably smart enough not to put baby stollers on a golf site and realize the affiliate either has another site that's a good fit or plans to build a new one around the merchant's products.
3) Some AMs screen out affiliate that have site that are new or don't have a certain
PR or a certain Alexa ranking or a certain CJ EPC. Again I think that's pretty narrow minded because everyone has to start somewhere and today's n00b could be tomorrow's super affiliate.
If you have another site that's targeted or plan to build a new site around the merchant then sending an email explaining why they should reconsider your app sometimes works. Also some apps have an open field where you can explain things like that to optimize your chances of being approved.
Realize that some of the bigger affiliate programs get 100s of apps a day, so it's hard to review them all and so some AMs just take a quick look at a bunch and decide they don't make the grade for whatever reason. So if it's a program you really want to join you make need to take the extra step to try to reach them and sell them on partnering with you.