First of all, he's showing a drawing of part of a flag of a foreign country, not flying it over the Capital building. Sheesh. If he'd just talked to the Japanese Diet, it would be the rising sun I expect.
Secondly he is not 3rd in line for the Presidency, nor in the line at all. He's House majority leader, 3rd in line is the Speaker of the House. Fourth is the President Pro Tempore of the Senate. I wish he was third in line, but he's not. The order, with more or less current officeholders is:
The Vice President Richard Cheney
Speaker of the House John Dennis Hastert
President pro tempore of the Senate1 Ted Stevens
Secretary of State Colin Powell
Secretary of the Treasury John Snow
Secretary of Defense Donald H. Rumsfeld
Attorney General John Ashcroft
Secretary of the Interior Gale A. Norton
Secretary of Agriculture Ann M. Veneman
Secretary of Commerce Donald Evans
Secretary of Labor Elaine Chao
Secretary of Health and Human Services Tommy G. Thompson
Secretary of Housing and Urban Development Melquiades
Rafael Martinez
Secretary of Transportation Norman Yoshiro Mineta
Secretary of Energy Spencer Abraham
Secretary of Education Roderick Paige
Secretary of Veterans Affairs Anthony J. Principi
It's a photo in which he has superimposed the Israeli flag over the Capital building.
If he'd just talked to the Japanese Diet, it would be the rising sun I expect.
In that case, show me an example. If this is standard procedure, then there must be hundreds of similar examples. I'll bet you can find the flags of dozens of countries flying over the capitol on official US government web sites. I'll be waiting to see them.
he is not 3rd in line for the Presidency
Check out the dozen posts that beat you to it.