I have also visited Bali many times over the last 10 years both before and after the two bombings. I agree that the island has a magical, spiritual quality that few other places I have ever been. Despite the two previous terrorist acts, Bali is still relatively safe; however, I was there in July 07 and noticed that it was very quiet with few tourists, and as a result I was harassed non-stop for transport, massage, drugs, watches, etc. I believe that most of these touts are from Java and not the local Balinese.

I did not experience as many problems while in Ubud.

I would definitely suggest Bali as a vacation destination but with the caveat of staying clear of the Kuta area. Bali has some beautiful beaches and great food (my favourite is Made's Warang in Seminyak) and the positive aspects are far more than the minor inconveniences. I think you would have a great time for your honeymoon.