Learn English – Is a scheme always negative in the US

Doesn't seem so. First of all it has another meaning

To agree with or be in harmony with

(TheFreeDictionary, near the end of page)

This meaning is obviously not negative

Returning to the meaning you had in mind. I didn't find any indication as to whether it is supposed to be always negative or not. It's nothing more than

To associate or begin to associate with

here or

Associate with, become acquainted with (especially by chance)

here From this definition fall in with implies accidental rather than negative nature of acquaintance.

Are allies always good guys? In theory, no. In practice, probably yes.

Most of the major wars (World War I, World II and others), involved LARGE groups of "allies" against a few countries that were also "allied." But the latter were widely perceived as the aggressors against the rest of the world, so few people outside these countries had much sympathy for them.

In practice, the large groups of countries tended to win most of these wars, and called each other "allies." Although they were technically "allies," the smaller groups of countries (e.g. Germany, Austria-Hungary, Turkey in World War I, and Germany, Italy and Japan in World War II) were instead regarded as "partners in crime" by most others.

It's largely a judgment passed by the international community, which is why the "allies" are usually considered good guys.