It appears as though George R. R. Martin discussed this in an interview with Entertainment Weekly back in 2011 before Season 1 was first aired.
This will be a big area of debate among your obsessive fans on the Web: What changes have you noticed the producers have made in your material?
There are changes, but I’m not sure how many of them are important. Like in the sets. The High Hall in the Eyrie, the one I described was long and rectangular with columns, and the one they built is round with curving staircases up. I had the Moon Door in the wall; they had the Moon Door in the floor. I know they tried, but they were not able to do the purple eyes for the Targaryens. You can do colored contact lenses, but that’s difficult for the actors and doesn’t always look right anyway. I have some great fans, but some of them get a little obsessive about things like that and are going to go crazy. But I’ve worked in Hollywood too long to worry about things like that. I’ve been on the other side of the process.
Entertainment Weekly, 'Game of Thrones': George R. R. Martin talks HBO show
As such it appears as though the reasoning is probably because it didn't look right and was uncomfortable for the actors. Whether the other reasons are true or not is unclear.
However, I have also found the following quote from George essentially stating he wishes he hadn't stated eye colours for everyone. As such it seems like that combined with the reasons above probably meant it didn't bother D&D anymore.
(17) Does he have a system for keeping track of his characters?
This is becomming increasingly more difficult for him. Most info is in his head. He does have family trees drawn up for the main families. But he finds himself having to keep going back and rereading his writing to find out info about his characters. He uses the "search" button on his books a lot. Computers and the "search" function make it a lot easier to find the info he is looking for. HE IS REALLY SICK OF EYE COLORS!!!!! He could tell everyone in the audience has eyes. However, he couldn't tell what color anyone has. You only really notice a person's eye color when you go in to kiss them. As a brown eyed person he gets really annoyed by the lack of brown eyed characters. Too much blue. And ff you have purple eyes...you are obviously important! He wishes he had never given any of his characters eye colors as he doesn't like having to keep that info straight. Instead he'd rather focus on things like a character's speach patterns. He likes to try and stay consistent to a character with that. Its important to him to keep a difference between the high born and poor people.
So Spake Martin, C2E2 Q&A
If you're wondering about what Dany and Viserys would have looked like if the show had used purple eyes it would be something like the following. The editors have added a very subtle purple hint to the eyes in the scenes and I must say it works very well. Obviously contains some spoilers as it is an edit of actual scenes so watch at your own risk.