Is his preferring to work with non-Muslims regarded as taking them as close friends?
Question

Is working in a company that is owned by a kaafir regarded as taking the kuffaar as close friends?.
Praise be to Allah.Working for kaafirs and doing business with them is not regarded as taking them as close friends, but the Muslim must be very careful in choosing the right type of people, work and business. It is not permissible for him to work with or deal in haraam things, and it is not permissible for him to love those people in his heart, or to praise them in absolute terms. He must also be honest and proficient in his work so as to give a good example of Muslim morals and manners. 
Shaykh Saalih al-Fawzaan said: 
The kinds of friendship that are forbidden include supporting them against Muslims, supporting them with words that justify their ways, and feeling proud of their ways. All of these are forms of the friendship with them that is forbidden and that leads to apostasy from Islam (Allah forbid). Allah says (interpretation of the meaning): 
“And if any amongst you takes them (as Awliyaa’ [friends and supporters]), then surely, he is one of them. Verily, Allah guides not those people who are the Zaalimoon (polytheists and wrongdoers and unjust)” [Al-Maa'idah 5:51]
What is permitted to us is to deal with the kuffaar in ways that are permissible. So we may engage in trade with them, import goods from them, trade benefits with them, benefit from their experience, and bring in those of them whom we employ to do different types of work such as engineering and other kinds of permissible work. These are the limits within which we are permitted to interact with them, but we must be cautious and not give them any authority in the Muslim lands except within the limits of their work. They should not have any authority over the Muslims or over any Muslim, rather the Muslims should have authority over them."(Al-Muntaqa min Fatawa al-Shaykh al-Fawzaan, 2/252)
Muslim bosses should fear Allah with regard to their work and their employees, and they should do work that is permissible. They should give their employees and workers their rights in full, with nothing lacking. They should not cause their workers and employees to leave them and go work for kaafir employers instead. 
Many Muslims think that it is the salary and other benefits that they get from the kaafir that is the motive for working for him, because they think that they are getting what they are entitled to. But this leads to bad consequences, such as praising those kuffaar and admiring their attitude and way of doing business. This may lead to taking them as close friends, which is a cause for fitnah (temptation and tribulation) for many of them with regard to their religious commitment after that. 
See the answer to question no. 2875 for the ruling on working for the kuffaar; and the answer to question no. 2371 where it states that it is permissible for a Muslim to work with a kaafir subject to certain conditions. 
And Allah knows best.