(UPDATED, with Asahi and New York Times join their colleagues.)
They must be feeling safe to report, because the scale of the protest was much smaller in the morning of June 16. 300 to 400 people showed up in the rain to protest the ministerial meeting that PM Noda was having at that time.
The Japanese mainstream media show no embarrassment for not having reported anything at all on the June 15 protest of 11,000 people. None of them even say there was a protest on June 15.
Who are they kidding? Majority of Japanese people whose sources of news are still traditional newspapers and TV, and/or who would rather not hear anything combative like a protest against a government policy.
TBS Television: http://news.tbs.co.jp/newseye/tbs_newseye5056988.html
Nikkei Shinbun: http://www.nikkei.com/article/DGXNASDG1600Q_W2A610C1CC0000/
Jiji Tsushin: http://jiji.com/jc/p?id=20120616122848-0012777847
NHK News: http://www3.nhk.or.jp/news/html/20120616/k10015874021000.html
Mainichi Shinbun: http://mainichi.jp/select/news/20120616k0000e040159000c.html
(UPDATE) Asahi Shinbun just joined: http://www.asahi.com/national/update/0616/TKY201206160158.html?ref=reca
Reuters is one of the very few news outlets worldwide who reported on the June 15 protest that drew 11,000 people:
...But the decision risks a backlash from a public deeply concerned about nuclear safety. As many as 10,000 demonstrators gathered outside Noda's office on Friday night amid a heavy police presence to denounce the restarts, urging the premier to step down and shouting "Lives matter more than the economy."
I heard that BBC also reported in the news program, but I haven't found it myself.
(UPDATE) New York Times joins the Japanese colleagues by only mentioning June 16 protest. See my post.