I thought this little application was supposed to be safe!?

I don't know much about that program, but it is certainly safe, what you have found are what people call false positives, this is almost certainly down to how the program works, because it is removing software from the system, various protection will flag it as bad, because it is typical of what happens when something is bad, the difference between the types of bad is quite simple, the real bad stuff does things without your permission etc, the false "bad" stuff is totally at your control, and only does what you ask it to do. What is suggested when such reports are found is to report them to the software makers, then if they feel they want to challenge the entry's they are fully entitled to, and as long as they can satisfy the places that have it flagged as bad are satisfied, they will then change the status of the reports, but it's not a quick thing, just depends on those involved as to when they have enough proof to make the change, so I hope this puts you at rest a bit, NO member here would knowingly suggest bad software, if they did they wouldn't be here for long, and given people who just look in like myself, if we saw something wrong we would sound the alarm bells, so hopefully you can rest easy now.

I think it is risky to use software which is more than 4 positive at virus-total, instead you can find alternatives for that program.