Along similar lines to the previous answers, my understanding of the medrash is that G-d did not create this world to exist as a self-contained one. Thus, while we see that indeed most creatures receive sustenance and offspring without engaging G-d through actual tefilla, this is not the ideal way of the world for which it was created. Rather this type of undeserved bestowal of good is part of the idea of "olam chessed yibaneh" - "world built with kindness" as a necessary prerequisite to achieve the actual purpose of creation, where man recognizes G-d and interacts directly with Him through the avoda and tefilla. If not for this ultimate din (give-and-take) level, nothing else would have been created. Thus, those who receive without any level of acknowledging G-d, are receiving in the same way animals receive their needs, in a role that is not the purpose of creation.
We find a similar idea in the contrast between the sustenance of Egypt, which receives its needs in a relatively predictable, closed system involving the Nile, and that of Israel, which is uniquely non-deterministic and unpredictable with regard to its weather patterns. As such, Israel is forced to acknowledge and engage G-d, thereby fulfilling theirs and the world's raison d'etre.
Another example is the way an infant's needs are provided for via unique and innate instincts and behaviors, such as sucking and nursing. As it develops and is able to fend for itself, these instincts and relationships are no longer the same source of nourishment.