Rina, I have a good friend who is Filipino, she is married to a Japanese man and she works for a Japanese company. I never heard her once complain about not being welcomed in Japan. She gets a long fine with the family and enjoys it very much in Japan.
I got to meet some of her friends, and her husband's friends, who were also married to Filipinos!
Of course nowhere in the world will people have a 100% positive experience. There are Filipinos who come to Japan and do have a bad experience. There are Japanese people who go to the Philippines and have a good time without problems, but there are people who visit the Philippines and have had bad experiences as well.
My Japanese friend was visiting Manila and said while he was waiting in the store, an old lady threw coffee at him and started yelling at him. He didn't know why, until another person told him it was because he was Japanese, and that old lady lost her husband during WW2.
Point of the story? For the most part most people have a positive experience when visiting another country (any country), but there are times when people do run into problems and these are generally the ones that write a lot about it, and the ones people search for and find stories about on the internet.