I doubt you put it out of line while working on the flat. It's possible that it got mis-aligned while riding with the almost flat tire before you noticed it. Or if it's only slightly out of line it's possible that when you repositioned the wheel it went back slightly to one side or the other and now rubs.
Step one, loosen and reposition the wheel with the bike on the floor and held straight up, letting the wheel find it's home spot, then retighten the QR or nuts. (If you have horizontal dropouts, you might have to hold it centered between the chainstays).
if that didn't solve it, and the total side to side wobble is less than 1/16" try re-centering the brake. If the wobble exceeds 1/16", consider having it re-aligned or DIY if you feel up to it. Here's a helpful site if you want to get started aligning your own wheels. My advice is take it slow and stay within your comfort zone.
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