Christianity was certainly present in Britain on a large scale by the end of the Roman rule over the island, but in the aftermath of the Germanic migrations into Britain much of the lowland parts of the island were now ruled by pagans. That's the tl;dr.

How however, did the presumably majority Christian population of Britain come to be supplanted by pagans? The old view of the Anglo-Saxons wading ashore and slaughtering all the native British and totally replacing them has long been discarded as a model for the Germanic migrations to what would become England, so if they weren't killed, what happened to them? After all England is a rather singular example of formerly Christian parts of the Roman empire having been conquered by pagans and abandoning the Church, at least among significant portions of the population. Robin Fleming argues that after the collapse of the British economy and the eventual removal of Britain from the broader network of the late Roman economic world, the island went into crisis and this is what ended urban Roman life on the island. Without trade to maintain the cities and Roman lifestyle among the institutions that withered on the vine was the Church, bereft of integration into the Roman economy urban life in Britain could not sustain itself and was eventually abandoned. Into this milieu of collapse, the pagan Anglo-Saxon kingdoms rose and for the formerly Roman inhabitants Christianity lost much of its appeal and cultural cachet. Paganism was now more advantageous for advancement in life, and as a part of the eventual assimilation of the newcomers and natives into Anglo-Saxon culture many native inhabitants abandoned their old religion.

This pattern however was not universal, some British polities were able to sustain themselves against the newcomers and Christianity retained cultural importance, similar to the adoption of "romanitas" across the rest of post-Roman western Europe, in these areas Christianity survived. According to our own source for the conversion of the Anglo-Saxon kingdoms though, the native British church had little impact on conversion to Christianity among the Anglo-Saxons, and credit is instead ascribed to Irish monastics and Papal missions. However, these Christian communities still survived in the highland regions of Britain, the Welsh and Highland Scots are the ultimate descendants of these people.

The Church never really went away in Britain, there is evidence of continual Christian practice in areas associated with Anglo-Saxon kingdoms and the surviving native British polities maintained Christianity has a marker of their own heritage. But among the rest of England now beset and ruled by pagans descended from migrators across the sea, Christianity lost its centrality and importance as well as its economic and social lifeblood once the British urban lifestyle collapsed as a result of the collapse of Roman power in the west.

A follow-up question: Were there any remnants of the original Roman/Briton christianity by the time the Anglo-Saxons were christianised, and if so, how did they react to or possibly aid the larger Christianisation of England?