That article is blatantly false and alarmist propaganda. It doesn't give any accurate context on the situation. Christian prayer is not and has never been labeled as Islamophobic and no one is saying that it is.
What actually happened in this specific situation is that on March 25th, Rep. Movita Johnson-Harrell, the first Muslim woman to join the Pennsylvania house of representatives was being sworn in to the house. Directly before this Muslim woman was sworn in, Rep. Stephanie Borowicz (a Christian) decided to say a prayer where she said things like "God forgive us — Jesus — we’ve lost sight of you, we’ve forgotten you"... Keep in mind that this is directly before a non-Christian person was supposed to be sworn in.
People obviously interpreted this as somewhat hostile towards other religions, specifically Muslims since a Muslim was about to be sworn in. It kind of seems like Rep. Borowicz is saying that this country has "forgotten Jesus" and needs to be "forgiven" specifically because a Muslim was becoming a representative instead of a Christian. And according to a
Times article on this incident, Rep. Borowicz "mentioned 'Jesus' 13 times, 'God' six times and 'Lord' four times. She also heralded President Donald Trump in the prayer over his support for Israel". What this shows is that her prayer was definitely meant to be a political statement and it was aimed towards Rep. Movita Johnson-Harrell in a way that was supposed to tarnish her achievement as the first Muslim representative. Rep. Borowicz made it all about herself and her own religion in a somewhat disrespectful way towards the audience which had many Muslims in it.
During her prayer Rep. Borowicz also said “At the name of Jesus, every knee will bow, and every tongue will confess, Jesus, that you are Lord". The article points out that: "the verse 'every knee will bow, and every tongue will confess' is often cited by Christians who argue that Christianity is the one true faith". Plus we all know that many evangelicals don't think that Muslims share the same God as a part of the abrahamic religions. So there's no way around this being a blatantly hostile statement in the context of that situation.
It's supposedly a common thing for the Pennsylvania House to open sessions with prayers and prayers from all religions are allowed to be made but they are supposed to be respectful of everyone's faiths. The chamber's normal protocol calls for an interfaith and respectful invocation... Borowicz didn't follow that and she was definitely not being respectful in her intentions with the prayer she made. Christian prayers are made every day and no one has a problem with that. The problem in this situation was not that a Christian prayed to Jesus... it's that Rep. Borowicz made a thinly veiled hostile political statement against the first Muslim woman who was being sworn in.
Rep. Movita Johnson-Harrell responded to this situation by saying: "It was directly a political statement, and I think we need to be very, very clear that everybody in this House matters, whether they’re Christian, Muslim or Jew, and that we cannot use these issues to tear each other down. And not only that, it was made during my swearing in".
Regardless of whether you think the prayer was meant to be hostile towards Rep. Movita Johnson-Harrell or not, no one has ever said that a Christian prayer is inherently anti-Muslim. People have labeled Rep. Stephanie Borowicz specific actions in this situation as insensitive and politically motivated but no one has ever said that Christians can't pray to Jesus in a positive and peaceful way. You are free to pray to Jesus as a Christian, no one has ever said anything different. You're not oppressed as a Christian in this country.