I found quite a few Confederate flags in museums of Northern States. Most of these prizes of war were returned long ago, but a few states never agreed to return their flags and still retain them. Here are some that I found with just a few searches. A few are for sale. The Museum of the Confederacy in Richmond has the best collection anywhere of Captured Confederate flags that were returned to Southern States and then donated to the museum. Maybe your ancestor's regimental flag is at one of these links. Enjoy!
http://historical.ha.com/common/view_item.php?Sale_No=663&Lot_No=72101&type=&ic=
http://historical.ha.com/common/view_item.php?Sale_No=674&Lot_No=72300&src=pr
http://www.civil-war.com/searchpages/confsearch.asp
http://images.google.com/imgres?imgurl=http://farm1.static.flickr.com/170/369532752_39c7215dd3.jpg&imgrefurl=http://civilwargazette.wordpress.com/2007/01/26/virginia-regimental-flag-captured-by-the-53rd-pennsylvania-infantry/&h=345&w=455&sz=59&hl=en&start=18&um=1&tbnid=eUV5uqASHQ-84M:&tbnh=97&tbnw=128&prev=/images%3Fq%3DCaptured%2BCivil%2BWar%2BFlags%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26rls%3Dorg.mozilla:en-US:official%26hs%3DF0R%26sa%3DG
http://images.google.com/imgres?imgurl=http://www.civilwargazette.faithsite.com/uploads/1143/46693.jpg&imgrefurl=http://civilwargazette.wordpress.com/2006/12/24/33rd-mississippi-flag-captured-by-stiles-brigade/&h=400&w=600&sz=33&hl=en&start=25&um=1&tbnid=6xNrN7WGT2R7xM:&tbnh=90&tbnw=135&prev=/images%3Fq%3DCaptured%2BCivil%2BWar%2BFlags%26start%3D20%26ndsp%3D20%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26rls%3Dorg.mozilla:en-US:official%26hs%3DWL7%26sa%3DN
http://images.google.com/imgres?imgurl=http://www.dmna.state.ny.us/historic/btlflags/infantry/gfx_inf/2ndMilitia82ndNYVIFlankMarker2005.0104.jpg&imgrefurl=http://www.dmna.state.ny.us/historic/btlflags/infantry/2ndMilitia82ndNYVIFlankMarker2005.0104.htm&h=300&w=389&sz=29&hl=en&start=37&um=1&tbnid=4BMHCbRQVrsE8M:&tbnh=95&tbnw=123&prev=/images%3Fq%3DCaptured%2BCivil%2BWar%2BFlags%26start%3D20%26ndsp%3D20%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26rls%3Dorg.mozilla:en-US:official%26hs%3DWL7%26sa%3DN
http://images.google.com/imgres?imgurl=http://www.kshs.org/exhibits/flags/graphics/199126lg.jpg&imgrefurl=http://www.kshs.org/exhibits/flags/flags2.htm&h=438&w=800&sz=135&hl=en&start=53&um=1&tbnid=VuWx-gFpmnd9AM:&tbnh=78&tbnw=143&prev=/images%3Fq%3DCaptured%2BCivil%2BWar%2BFlags%26start%3D40%26ndsp%3D20%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26rls%3Dorg.mozilla:en-US:official%26sa%3DN
Flag captured by the 2nd Delaware Cavalry, Lt. William Bird below link
http://www.horsesoldier.com/catalog/444-01.JPEG
Flag captured at Fredricksburg by the 4th Michigan below link
http://images.google.com/imgres?imgurl=http://www.4thmichigan.com/images/National%2520confederate%2520flag%2520captured%2520at%2520fredericksburg,%2520Va.jpg&imgrefurl=http://www.4thmichigan.com/The%2520Seages_Papers_%2520and_Memorabilia_.htm&h=256&w=341&sz=12&hl=en&start=7&um=1&tbnid=SLY0sPUOFMGcyM:&tbnh=90&tbnw=120&prev=/images%3Fq%3DCaptured%2BConfederate%2BFlags%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26rls%3Dorg.mozilla:en-US:official%26sa%3DG
http://images.google.com/imgres?imgurl=http://www.jeffbridgman.com/inventory/files/flags.553.1.jpg&imgrefurl=http://www.jeffbridgman.com/inventory/index.php%3Fpage%3Dout%26id%3D189&h=526&w=700&sz=95&hl=en&start=50&um=1&tbnid=YGeUbdP1Rxxh4M:&tbnh=105&tbnw=140&prev=/images%3Fq%3DCaptured%2BConfederate%2BFlags%26start%3D40%26ndsp%3D20%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26rls%3Dorg.mozilla:en-US:official%26sa%3DN