Every time science has explained something previously attributed to God, from lightning to disease to the origin of species, the explanation turned out to be natural, so invoking God for remaining gaps like the origin of the universe or consciousness is just repeating a losing pattern.

Why people find it persuasive

The history of the God-of-the-gaps move is a history of retreat: gods explained weather, disease, the sun's movement, and the diversity of species, and every single one of those has since received a thoroughly naturalistic explanation. Betting that the pattern will finally break for the remaining unexplained gaps looks like special pleading born of not wanting to give up the last redoubts.

Important distinctions

• • Arguments that plug a temporary explanatory gap versus arguments based on the very existence of an explicable, law-governed universe at all
• • Local, empirically closable gaps (why does lightning happen) versus boundary questions science is not built to address (why is there something rather than nothing)
• • God as a competing causal mechanism within nature versus God as the metaphysical ground of nature's existence and intelligibility
• • The historical pattern of specific gaps closing versus the claim that all possible gaps must eventually close
• • The origin-of-universe and fine-tuning arguments versus classic 'God did the thunder' folk explanations

Christian response

• • The objection has real force against a certain kind of argument: historically, some apologists did point to specific unexplained natural phenomena (disease, weather, planetary motion) as direct evidence of divine action, and those gaps were subsequently closed by science, embarrassing that style of argument. Philosopher and theologian Dietrich Bonhoeffer criticized this very move in his 1944 prison letters, warning Christians against 'using God as a stopgap' for the temporarily unknown, arguing this both makes bad science and bad theology.
• • But the best contemporary theistic arguments, such as the kalam cosmological argument or fine-tuning arguments defended by philosophers like Robin Collins and William Lane Craig, are not of this form. They do not point to a temporary hole in scientific knowledge and insert God; they point to features that persist and even sharpen as science advances, such as the universe having an absolute beginning (supported, not undermined, by Big Bang cosmology) or the extraordinary precision of physical constants (which became known through, not despite, increasingly precise physics).
• • There is a difference between explaining a mechanism within nature (how lightning forms, which meteorology now answers) and explaining why there is a law-governed, contingent, intelligible universe capable of producing lightning and meteorologists at all, which is a question no amount of physics answers by definition, since physics presupposes the existence of physical law to operate. Philosopher Richard Swinburne, in The Existence of God (1979/2004), argues theism functions here as a personal explanation of the universe's existence and order as a whole, a different logical category from a scientific mechanism explaining one phenomenon within it.
• • It is also worth noting the pattern runs both ways rhetorically: pointing to past retreats of 'god of the gaps' arguments does not itself establish that every remaining question, including boundary questions about existence and consciousness, must have a purely naturalistic answer; that is an inductive extrapolation, and a reasonable one to weigh, but not a proof, since the questions at the boundary (why anything exists, why the universe is comprehensible, why consciousness exists at all) are different in kind, not merely in current difficulty, from mechanistic questions like weather formation.
• • The honest position is that theists should avoid inserting God into merely temporarily unexplained mechanisms, and many serious philosophers of religion today, including Alvin Plantinga, explicitly reject god-of-the-gaps reasoning while still defending cosmological and fine-tuning arguments precisely because those arguments are not of the gap-filling kind.

Christian counterresponse

That is a live possibility and a legitimate reason for humility, but it cuts against overconfidence on both sides rather than uniquely against theism; it is equally possible current naturalistic assumptions about a self-existent, brute multiverse or self-caused initial state turn out to be as unstable as any theistic gap-filler, so the honest response is proportioned confidence pending further evidence, not a presumption that naturalism automatically wins every future round.