So I'll try to explain, as simply as I can (since more depth would require textual analysis of his works that is lengthy), why Pappé is typically not regarded with favor amongst historians.

Pappé, while a historian by trade, does not typically come to conclusions made by other historians, American, Israeli, or otherwise. There is a political flavor to his work, so to speak, which is why there is criticism of him based on political opinion, as you've observed.

Part of the problem is simply that of interpretation. Pappé is so far from the original, traditional explanations Israeli historians gave for things like the Palestinian refugee problem's origins, that he stands at the extreme of conclusions based on documents others have read. As a New Historian, it's normal to deviate from the norm: others like Simha Flapan and Benny Morris do the same. But they are not criticized nearly as heavily, despite drawing conclusions that traditional historians did not (partially out of wanting to help Israel's image, partially because they didn't have access to documents the New Historians do). So, when Simha Flapan, Benny Morris, and Ilan Pappé see the same document archive, they all disagree on what the conclusion of those documents (as far as things like responsibility and actions undertaken) means.

Take the refugee problem. Each of those three sees a different level of centralization in the destruction of Arab-Palestinian villages, and the use of expulsions to clear them. And all of them are likely looking through the same documents to come to those conclusions. What makes Pappé stand out is that he typically assumes the worst of Israel (it doesn't help his reputation that he studied under an Arab historian, who people feel brainwashed him, though historians don't really use that line). He also uses politically charged language, which is something historians typically try to avoid. Using terms like "Ethnic Cleansing" in the title of his book exactly explains how he seeks a political reaction, and he attempts to justify it by comparing the situations to those in Yugoslavia in the introduction to his book. However, the situations are entirely different, as most people are aware: it appears to most historians that he is trying to use political charged phrases to gain attention and readers.

Because of this political atmosphere, he gets a lot of political criticism. Compare his works to those of Benny Morris, who also gets political attacks from both sides of the Palestinian-Israeli conflict, and you'll note that Pappé is much more controversial to Israelis, and much less so to Palestinians. It's all about where he falls on the scale, the wording used, and the interpretations he draws. It's hard to say if he's "right", because a lot of the documents are reclassified now, or are hard to access if you're not in Israel and doing extensive research. However, Pappé is typically looked down on by historians as well because of the more extreme conclusions he makes, and because of his political undertone as perceived by them.

Hopefully that explains. If you'd like to see a comparison of Morris, Flapan, and Pappé on the creation of the Palestinian refugee problem, feel free to check out my post here that sums up their views. It's a tad lengthy, but will give you a comparison to judge off of that explains my view as well.