Pennsylvania's governor and the mayor of Pittsburgh declined to join him during the visit.
"President Trump's words, actions and policies have espoused and emboldened the type of violence and hatred our community so tragically endured with the massacre of 11 Jews in their place of worship", one group organizing the protest said on Facebook.
Dr Jeff Cohen, was interviewed by Channel 4 News about his experience of meeting the man who killed 11 people at the Tree of Life synagogue in Pittsburgh on Saturday, where he himself is a parishioner.
"I'm a citizen, and he's my president, he's certainly welcome", Myers said on ABC's Meet the Press.
Two men embrace as they arrive at the Rodef Shalom Congregation where the funeral for Tree of Life Congregation mass shooting victims Cecil Rosenthal and David Rosenthal was held.
The brothers were widely known as "the boys", the Rosenthals' sister, Diane Hirt, noted. The president wants to be there to show the support of this administration for the Jewish community. He said the president is welcome in his city anytime.
"I'm focused on family and community".
A line stretched around the block as mourners - some in white medical coats, some wearing yarmulkes, black hats or head scarves - passed beneath the blue Romanesque arches into the brick building.
"Every time our country has experienced the type of heartache and pain that we have over the last week, this is a president who has risen to that occasion", Sanders said.
"A lot of people are feeling really angry about this". Those charges include 11 counts of criminal homicide, six counts of aggravated assault, 13 counts of ethnic intimidation, as well as firearm and hate crime offenses. "It's just such a loss".
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Services for 66-year-old doctor Jerry Rabinowitz and 71-year-old Daniel Stein followed in Pittsburgh, where scores of residents protested Trump's visit.
Trump's visit generated controversy in Pittsburgh, where some said the president was welcome and others insisted that he stay away.
At a memorial outside, the first lady placed a flower and the president laid a small stone on a marker for each of the victims.
Trump will travel to Pennsylvania on Tuesday with first lady Melania Trump.
Hundreds of protesters gathered near the synagogue and the hospital. "And he's ... people say that he's evil, he's this ... he's some mother's son".
"It was not the face of villainy that I thought we'd see", said Jon Pushinsky, a congregant at Dor Hadash, which lost one of its members to the massacre.
Other locals said they will survive this incident and be stronger because of it, but will never be the same.
Trump's visit to the city has been contentious, coming amid a mounting row over whether his fierce rhetoric at campaign rallies and on Twitter has helped stoke extremism ahead of November 6 midterm elections.
As he stood in line at the funeral, Friedman wondered why he had been spared. "I got to know him there".