13 It may be also understood in this way: “The poor ye will have always with you, but me ye will not have always.” The good may take it also as addressed to themselves, but not so as to be any source of anxiety; for He was speaking of His bodily presence. For in respect of His majesty, His providence, His ineffable and invisible grace, His own words are fulfilled, “Lo, I am with you always, even to the end of the world.” But in respect of the flesh He assumed as the Word, in respect of that which He was as the son of the Virgin, of that wherein He was seized by the Jews, nailed to the tree, let down from the cross, enveloped in a shroud, laid in the sepulchre, and manifested in His resurrection, “ye will not have Him always.”
And why? Because in respect of His bodily presence He associated for forty days with His disciples, and then, having brought them forth for the purpose of beholding and not of following Him, He ascended into heaven, and is no longer here. He is there, indeed, sitting at the right hand of the Father; and He is here also, having never withdrawn the presence of His glory. In other words, in respect of His divine presence we always have Christ; in respect of His presence in the flesh it was rightly said to the disciples, “Me ye will not have always.”
In this respect the Church enjoyed His presence only for a few days: now it possesses Him by faith, without seeing Him with the eyes. In whichever way, then, it was said, “But me ye will not have always,” it can no longer, I suppose, after this twofold solution, remain as a subject of doubt.
Source: Tractates on the Gospel of John (New Advent)