Toilet lid covers are not, in and of themselves, bad things.
I have one on my toilet lid in my master bath, and I have it there for a reason: when I get out of the shower, I want someplace to be able to put my foot while I dry off my legs and haunches, and I don’t want it to be someplace slippery.
The trick is to get one that’s not so fluffy that it causes the problem described by the OP.
I’m so glad my husband sits down to pee. We don’t have to deal with mis-aim or anything in our house.
That said, seat covers are gross 
So does he hike up his skirt first, or just drop it to the ground?
Does the bathroom have a shower stall (or tub even) if so, problem solved. IT’S ALL PIPES!
I had a nice, fluffy toilet seat cover that matched the throw rug and all that, but I don’t use it because my husband complained of the same problem (seat won’t stay up) and I’m a reasonable woman. 
ETA:
Forgot to say, this is called an en suite bathroom, or just an en suite. We have one because of our cats - they get all excited when we come out of the bedroom in the middle of the night to go pee, because, HEY! PLAY TIME!
Ugh. We have no frilly seat cover, but we do have one of those cushy seats. An evil, evil cushy seat.
It lets the seat drop sometimes. Weeks can go by with nary a fall. By that time I’ve let down my guard and occasionally don’t stand there all contorted, bent halfway over with fingertips holding the chomper back. Then WHAM! (typically at 3AM).
Evil, evil seat.
Tell her if she does not get rid of the cover, you are going to hang the toilet paper the wrong way. She’ll back down.
We threw away everyone of these we ever tried (having forgotten about the earlier tries).
I have a solution - Velcro. Just have to be careful where you sit. BTW, it’s a lid not a seat.
Oy, the thing that makes it sound like you’re full of gas before you even do anything…
Ah, the dreaded Sitzpinkel!
I grew up in a house with two sisters. I’m housebroken. But, even though I’m on the wrong side of 40, I still sometimes wake up with morning wood. Which makes it impossible to sit down and pee. Any attempt to sit and pee with an erection will result in urine on walls and towels rather than just the seat.
If I were building my own house, I would definitely install a urinal. And a bidet.
No need to wait to build a house for that bidet. $99 gets you a great one: http://sanicare-bidets.stores.yahoo.net/acehsbidet.html
We have them on our toilets.
Mr Modesty here needs a whole hand for job one?
I hold the clothing out of the way with the heel of my hand and aim using the rest. It’s simple, or to use the vernacular, a piece of piss.
When I was a kid, I always used to dream of building my own house so I could just build a little door right beside the bed; I could just roll over, open the little door, pee into the back yard, close the door, and go back to sleep.
Doesn’t work with elastic band waists (shorts, jogging pants, jammies, etc). You think everything is held just right, and then the elastic snaps out of your grip and squishes Fireman Joe in an unpredictable direction. Believe me, you don’t want to be the one having to figure out how to clean urine out of the scented candle receptacle.
I’m going to save your marriage. I just replaced my toilet seat, and got one, for fun, which has a slow closing feature.
Here is the first result from Googling toilet seat slow closing.
When you push it closed, it can take a few seconds to go down, more than enough time to push it back up - or maybe even finish.
For the not-enough-hands guys -
Why not just drop trou, one hand on the seat the other aiming Mr. Happy, do your business, then pull up trou?
I can see why you wouldn’t want to do this in a public urinal, but hey - you’re at home, you can close the door, and your wife has presumably seen your ass before, right?
We solved that by replacing the (cracked) bowl with an elongated one. With the “alcoholic” open front. Accommodates the entire package.
That’s what your balls are for. :rolleyes:
Testicles, decorative and functional! 
CMC fnord!
My local Humane Society uses those lid covers as cat beds, and has them on its wish list. Apparently, they are just the right size and shape for a regular sized cat to curl up on. The part that normally goes on the underside of the lid makes a sort of ledge, so the cat feels all comfy and secure in a nest. Your local HS might very well be happy to take your lid cover from you, assuming that it’s been in the washer and dryer since you peed on it.
For those who didn’t click the link, it’s a 3-page PDF well worth the reading.
I’m going to suggest that the male hate for toilet lid covers seen here today is the mirror image of the oft displayed female hate for men leaving the seat up. In each case we have something which generates no downside for one team while creating a downside for the other. And a downside the first team for whatever reason can scarcely comprehend.
I don’t like toilet seat covers, but just because I have a dislike for anything which is both purely decorative and impedes the function of whatever it works with.
e.g. … Fancy drapes? Like 'em just fine. Fancy drapes which only retract far enough to reveal half the window & the beautiful view outside, which is further obscured by a fancy valence thing covering the upper third of the window? Out with the trash.
Toilet seat covers which don’t make the lid fall down? Pointless, but harmless. Covers which do? Out with the trash.