While your point is a well-founded reminder that this country has always had christian roots, I don't think that the "in god we trust" references necessarily invoke the endorsement of any one religion. Every religion that I know of believes in god in some sort. However, I think it is a different thing to have a symbol of one religion's winter holiday without acknowledging others.
Our local courthouse has two christmas trees, and I am almost certain that the county paid to have them there (I personally watched county employees setting it up). When in a government building that is paid for by all taxpayers (not just christians) I personally am a fan of having a display that recognizes the cultural celebrations of all faiths. For instance, I find that having a display of a menorah, christmas tree, candle display, santa, etc. promotes a feeling that all beliefs and all holiday traditions are valuable and are part of the overall holiday spirit.