Or when the atheists go on their rant when the opposite happens?
I haven't heard of any atheists trying to boycott stores for having signs saying Merry Christmas, have you? I think you would have a hard time finding any atheist who would get upset by public employees, at their own expense, decorating their offices with Christmas displays. As long as it's not at public expense, and as long as the guy who puts up the Hanukkah display, or the one who puts up the Muslim display, at their own expense, are allowed to do so as well.

There are always two sides to the coin....I'm just betting there are a number of factors other than religious affiliation that influenced that judges decision; despite the one sided article's presentation of it.
Yes, there were. If you read the Court Order they list 13 different items that the judge base his decision on. Among them:
"8. There was evidence that the Respondent/Mother had left minor children at home alone, did not feed them breakfast, and did not at time buckle them in their car seats."
and "10. Further evidence indicated that the Petitioner/Father did not participate in the same religious training that the Respondent/Mother exercises and that the Petitioner/Father was agnostic."
and "11. There was evidence that the Petitioner/Father did involve himself in the children's activities."
and lastly, "13. There was evidence that the Petitioner/Father did use profanity in the presence of the children and at time failed to control and manage his anger."
My point is, why should his religious affiliation matter in the least? Nothing there said that his anger and profanity were even directed towards the children (likely directed at the mother, would be my guess), while her routinely leaving them home alone, without breakfast, and risking them while driving would certainly make me think twice about trusting them to her care.

In the US, any group can apply for permits for public celebrations, and pay the required fees.
So if they do then let them be!
I challenge you to show me where atheists have disrupted or harassed Christians who were gathering legally for some kind of celebration or event. Yet who are the primary instigators at, for example, LGBT parades, or military funerals?

You asked what atheists celebrate instead of Christmas. (the birthday of their atheist sophist savior perhaps? whats his name, oh thats right Hutchinson or something right?)
I don't even "celebrate" my own birthday! Why would I want to celebrate someone else's?