• In England, where the 58% of the cases that get to court result in a conviction, there is a common perception of lack of prosecution which deters people subjected to sexual assault from reporting sexual assault crimes.  (via)
• Even when reported, rape kits often go untested due to costs. It can cost up to $1,500 to test a rape kit. LAPD, for example, eliminated its backlog of rape kits in 2011. Over 6000 rape kits were sitting in storage while over 6000 rapists were walking around. (Of course, this does not mean that 6000 rapists were convicted—only about 1000 matches were made and many were already prosecuted). Courts may miss crucial evidence because of costs associated with testing.
• In the European study cited above,  lack of training and technology is cited as a reason why a small number of cases gets prosecuted. Under-reporting, victim blaming, and inadequate data are also cited. (rcne, page 14). Given the data available, it is easy to conclude, as the authors of the study do, that there simply hasn’t been an allocation of resources to increase tools and training available. 
• Rape victims are expected to act a certain way. For example—

If a rape victim has “consensual”, or coerced but non-violent sex following the rape it makes it harder to prosecute. When it comes to sex crimes or sexual behavior, the average person/jury member can’t seem to comprehend nuance. If you are raped, you should diligently scream and struggle in just the right way, call the police, collapse in a ball, and never have sex again. If you deviate from this script or course of action, well, you didn’t fight hard enough. You weren’t actually raped. There are many reasons why a victim may have sex with her rapist again following a rape - possibly because she is not safe, and can’t say no without escalating the situation into more violence. Possibly, because there’s so much confusion that comes with an assault, she’s trying to comprehend what just happened. The victim may be trying to talk herself out of it “Ok, did that really happen? Did I imagine it? How could something have snapped and changed so quickly? What did I do wrong? Maybe I can fix it or make it better.” That’s common, too. (via)

• Because of rape culture, in which violence is perceived as something that’s sexy or desirable. (yes, it can be, but only and ONLY when explicit consent has been given)
• In cases where the rapist is someone close to the victim, it is difficult for the victim to come forward
• Personal belief: Because rape is often something that happens behind closed doors, it is often regarded, wrongfully, as an “he said, she said” issue. And since we live in a society that loves engaging in victim blaming (See below), a rape survivor’s words that they were abused often fall to deaf ears. If a jury is to decide a rapist’s fate, our society has taught for generations to blame the victim. 
• And last, but not least, because you have assholes like Rick Santorum that believe that rape victims should really just stop complaining about wanting an abortion and make the best of the situation

As a final note, RAINN has an extensive list of suggestions to reduce sexual assault, none of which is NO MEANS FUCKING NO, DON’T FUCKING RAPE. 

(PS: I know that this answer is in no way complete. I started out by putting together statistical evidence as to why rape cases are under-prosecuted and got a little carried away. I have placed every trigger warning tag I could think of, so please keep them when reblogging)