Microsoft Security Essentials doesn't really scan for, nor really catch, anything other than actual virus activity - it's not necessarily a full-on malware scanner, as it's tuned more towards detecting things like rootkits and malware that does virus-like activity (drive-by installers, etc.). One other thing to note is that MSE is not the same as Windows Defender in Windows 8 and 8.1 - Windows Defender uses the same update/scan engine, but it scans for or tries to protect from more than what MSE does. They're similar, but not the same, and while MSE is what someone using Windows 7 here would use, it's worth noting that Windows 8/8.1 does have something a little more advanced built in. AV Comparatives don't test Defender, they test MSE, and I'd guess partially because you need Windows 8/8.1 to get the advanced Windows Defender engine, whereas if you're on Windows 7 or lower you're stuck with MSE.
In general, while MSE is great at protecting a machine once clean (and it does a damned good job when used in an offline scan of an infected one), it's not perfect if you want something full-featured. Admitting that up front is the best way to approach any security product - what does it do, what does it not do, and does it do what it does well. Looking at what MSE is good at, it scores very well -
Microsoft Goes From Cellar to Stellar in New Antivirus Test - but as an overall security suite, it's not very good when compared to products that do a lot more.
AV Comparatives gives MSE a relatively poor overall rating specifically because it's not a full-featured product, and when compared against those types of solutions it's most certainly not going to score well. I think some people equate that with "MSE must be bad!", when that's not exactly the case (again, it's a
minimally-featured product designed to protect people who don't ever think about this, or who got that OEM trial and never updated it or paid for it, etc. - even Microsoft admits this and recommends something more thorough if you want or need it). It can be used as a primary product if you're already careful, but if someone is expecting it to behave the same as some of the more well-known and full-featured antivirus/antimalware products, then yes, there's going to be a problem (perception or otherwise).
There's nothing wrong with that, and there are lots of great products out there that are probably better overall if that's your goal. However, I find MSE + MalwareBytes + CCleaner to be good enough for me, but I don't do a whole heck of a lot with the PC either (some email, basic web browsing to specific sites, and gaming).
