Romanticism always raises the thorny question of "Spiritual or Religious?" With some Romantics, like that atheistic rebel Percy Shelley, the answer is easy. With Coleridge, it's not. In "This Lime-Tree Bower My Prison," Coleridge clearly does not sound like an orthodox English Protestant or Catholic, and he even needles Christian churches at one point. But the intensity of the poem's spiritual imagery makes the modern distinction between spirituality and religiosity seem more than a bit limiting. It might help to remember that Coleridge was an inspiration for the later American Transcendentalist movement, which took the view that reality was a unity behind the veil of nature's diversity. Ralph Waldo Emerson and Henry David Thoreau were two of the major figures of American Transcendentalism.
"This Lime-Tree Bower My Prison" is an example of "Natural Supernaturalism," where Christian images and symbols are transposed onto nature.
The viewpoint of the poem is fundamentally Pantheistic – it argues that "God is everything, and everything is God."