If its true that they penalized him just for prostrating then that is truly sad and hypocritical on the part of the NFL.
But, anyway, this should be of interest:
In the Sunnah, the Prophet (peace and blessings of Allaah be upon him) said: “I disown every Muslim who settles among the mushrikeen.” Narrated by Abu Dawood, 2645; classed as saheeh by al-Albaani in Saheeh Abi Dawood.
When you immigrate to non-Muslim countries and then pray in public (keep in mind though, Muslims are allowed to practice their faith in privacy or in a mosque BTW), then you shouldn't be surprised of such a reaction.
And when i see Pakistanis or any other Muslims cry rivers over little incidents like these i fail to see how they overlook the treatment of Christians and other religious minorities within Pakistan and other Islamic countries. Seriously?? You treat your own minorities like second/third class citizens but cry rivers when even the slightest wrong is done to you in a non-Muslim country?? Hypocrisy at its best i tell you.
