I think so too, even though Pipin is always getting in trouble (the palantir later, etc.).
It was, IMO:
1) Because of his (and Merry's) innocence.
2) Because Elrond's heart warned him that there would be trouble in the Shire. He wanted Merry and Pippen to be messengers to warn and deal with whatever troubles were brewing in the Shire.
However, I would agree that it was mostly the matter of Merry and Pippen's innocence and I think perhaps Elrond didn't think they would contribute enough to the Fellowship to warrant their inclusion: they didn't bring any unique skills/abilities to the Nine Walkers...at least none that were immediately apparent to Elrond.
Of course, we all know that Gandalf successfully argued for their inclusion and the reasons he gave for doing so. It is another example of Gandalf's great wisdom and foresight.
Tuor