Does 'fall in with' always have a negative connotation?

Often people say,

he fell in with a bad crowd,

meaning that the person happened to form relationships with an undesirable peer group or group of people.

Does the term 'fall in with' always have negative connotations?

Could you:

Fall in with a group of classicists or knitters?

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.

Short answer: No, fall in with doesn't always have negative connotations.

Long answer: Google returns tens of thousands of results for "fall/fell in with a good crowd", and it's pretty obvious they're not all ironic.