Dr. Bilal Philips mentions that not all shi’ahs are out of Islam. Only a minority of scholars have declared so, wherea the majority of the scholars hold the opinion that they are just a deviant group (some group among shi’ah are considered as kafirs by all the scholars).

In fact, Dr. Bilal Philips said “no” when asked if prayers behind a shi’ah imam is invalid. Please explain this opinion.

Yes, you are correct concerning making takfeer of the Shi’ah, there is a difference between the groups among them. Please see:

http://www.islamqa.com/en/ref/97448

Concerning what Dr. Bilal mentioned regarding praying behind them, then this is not correct. The correct position is that it is not permissible to pray behind a Shi’ah Rafidhi Imam. And this is the position of a large number of scholars of Ahl-us-Sunnah. Here’s Sh. Bin Baz’s fatwa on the issue:

With regard to praying behind one who is of this nature, Shaykh Ibn Baz (may Allah have mercy on him) said:

“It is not permissible to pray behind any of the mushrikeen, including those who seek the help of anyone other than Allah and seek support from him, because seeking help through anyone other than Allah, such as the dead, idols, the jinn, etc. is shirk, the association of others with Allah, glorified be He.”

Fataawa al-Shaykh Ibn Baz (vol. 2, p. 396)

And he said: “One should not pray behind any imam who is known to exaggerate concerning the Ahl al-Bayt (members of the Prophet’s household). If no such thing is known about him or any other Muslim, then it is OK to pray behind them.”

Fataawa al-Shaykh Ibn Baz, (vol. 12, p. 107)