Objections to Scientology are not (for the most part) based on their religious beliefs, but their practices and behaviors. They have a history of being aggressively litigious, similar to patent trolls[1], and have used frivolous lawsuits to harass critics into giving up the fight. There are also some indications that they're emotionally abusive to their members, and encourage them to cut off all contact to non-Scientologist friends and family. These allegations are difficult to substantiate, in part because the Church is so aggressive about quelling criticism.

In general, the Intarwebs regard Scientology as an organization that invests substantial financial and legal resources in limiting free speech on the internet. This is generally unpopular, regardless of who is doing it. The Church's status as a religious institution is largely immaterial to this perception.

[1] Very similar, actually. They claim copyright on their religious writings, and use that to sue people who release them.