In the books I think GRRM had second thoughts on presenting this relationship as harshly as he perhaps should have and tried to soften it, which was a mistake as it leads to a mixed message. In the TV series the producers make it abundantly clear that it's rape and it is not pleasant (their commentary on the issue on the DVD commentary is quite interesting). They definitely did not want to appear to be condoning it.

That said, there is some logic in GRRM's approach as well. As we are told in her first chapter, Dany sees herself as a good girl who does what her brother, the head of her house and the person who has protected her all her life, wants. There's also the whole honour of the house thing which is less important to her than Viserys, but still there. Dany's journey in AGoT (and much moreso in the following books) is moving from believing she can only affect things by playing by the role society assigns her - getting married and having kids - to the realisation she can exercise her own power and do things the way she wants, even change the world (and she does this even before she gets the dragons, although they do make that approach easier). Having to live with being married off to a barbarian warlord at her brother's command is the start of that journey.

Where GRRM softballs it is by making Dany actually fall in love with Drogo. The TV series seems to be suggesting at one point that it's more of a case of Stockholm Syndrome (the actors playing Jaime and Cersei actually debate this briefly on the DVD commentary as well), though they also seem to back off from that by the end of the season. Having Dany constantly disliking Drogo may have been more interesting, but it also may have backfired, as the readers then wouldn't have cared when he died.