Thanksgiving is a great holiday. Any day is a holy day, if it engenders some reflection on the good things--gifts, really--in our lives. I know--I am totally convinced--that I have more things for which to be thankful than I can take time to enumerate. This is why a day set aside for reflection on these matters is a blessed moment in our too-busy lives.
The fact that America began as a project to dominate the continent--both nature and people--is worth remembering and reflecting upon. Hopefully, instead of engendering guilt, it will inform changes in our national project, a project to respect peoples and live with, not against, nature.
I would like to see (I have not seen this advocated anywhere else) a national Native American Day, when we acknowledge and fully explore and remember the contributions to American culture and the unsanitized history of genocide perpetuated against Native Americans. Then, we could have BOTH a day of difficult truth-telling (which might help us rectify past wrongs and to heal and to understand America in completeness) and a day of Thanksgiving.
America, as is any individual, is both honorable and good and also has had--and still has--its egregious faults. At some future time when we as a nation see, understand, and act upon both our positives and negatives, that will be a time when we can give some extra thanks.