This expression has been used by people with radically different perspectives. It does not have to mean that one denigrates scripture at all, even though some may use it this way. The notion is also found in the original preface to the King James Bible, and is found as far back as Augustine. As for me, I like the expression. As I use it, I mean that although the Bible is our ultimate authority, it is not our only authority. I believe in sola scriptura, not nuda scriptura. One way of looking at this is in relation to Barthianism: Karl Barth did not have a very high view of general revelation. To him, the existential experience of God as one was confronted by the Word of God was all that mattered. But that is to go beyond what the scriptures teach: there is general revelation (God reveals himself in nature, conscience, and history) that is God's truth. To be sure, it cannot be interpreted accurately without the filter of scripture, but it is there nonetheless. When we don't allow for such a maxim as "All truth is God's truth," we may be shortcircuiting the very means by which God expects us to learn of him.
In other words, I would use the phrase but explain it. Scripture above all other sources of truth, but not scripture alone as a source for truth.