Advert companies like AdWords tend to rely on contextual advertising i.e the advert shown to user is relevant to the content its being displayed around. The problem comes if the advertising company can't see the content they can't pick an advert to show the end user.
In addition most have strict rules on placement of their adverts, number of ads being displayed etc. The problem is behind a wall they can't see if you are following the rules and it's simpler to say no then to trust you.
While you will have to do some research you are probably better of looking at the smaller display networks which may have less stringent rules or networks where the advertisers rather then the network decide where ads are shown.
That said I do think ultimately you may have more success with affiliate marketing not least because you will be better able to tailor the adverts to the content but also because most affiliate programs will not mind seeing traffic from behind a walled garden.
Disclaimer: I work for a company that builds an ad management plugins/systems