Marc Albrighton put the visitors ahead after 33 minutes before Stylian Petrov's hopeful strike deflected in off former Villa defender Gary Cahill.
Ivan Klasnic pulled one back for the Trotters after the break but Alex McLeish's side were able to hold firm for their first away win of the campaign.
The result was Bolton's seventh defeat in eight league games at the Reebok and the home fans roundly booed their side off the pitch at the final whistle.
Coyle groaned: "Disappointment is an understatement. We were at home and looking to win the game and start moving up the league.
"It is a horrible feeling. I thought the game started evenly with two teams looking quite nervous but then we conspired towards our own downfall.
"Aston Villa have some very good players but we made four or five individual mistakes within the first goal ? it was self-inflicted.
"Then you are looking for a reaction, for people to show a bit of guts, desire and hunger for the football club.
"But if the truth be told, for a few minutes, they looked as if they felt sorry for themselves and that allowed Villa to get a second goal.
"It is a good strike from Petrov which has hit Cahill and spun in but if we had been shutting down that wouldn't have transpired.
"At half-time I asked, if nothing else, for them to show that they care for the club in the second half ? and they did that.
"There were still some mistakes but it was a much better performance and much more like ourselves."
It was Bolton's first appearance at home since the passing of former midfielder Gary Speed and respects were paid before kick-off with a minute's applause.
Brad Guzan made his first Premier League start for Villa in the absence of the injured Shay Given and was tested early on with a Cahill header.
Petrov then had a great chance to open the scoring but shot wide when through on goal after a Charles N'Zogbia cross.
And Darren Bent should have put Villa in the lead but saw his effort come back off the legs of Jussi Jaaskelainen.
The visitor's pressure eventually paid off just after the half-hour mark when Gabriel Agbonlahor skinned Dedryck Boyata before playing the ball back to Albrighton who fired in from 10 yards.
It was Villa's first league goal in four games and their second came just six minutes later thanks to an own goal from their former player Cahill.
Petrov picked the ball up 30 yards from goal and with nobody closing down, tried his luck and saw his drive go past Jaaskelainen after a wicked deflection off the England centre back.
Bolton almost pulled one back two minutes before the break but Guzan did well to block Kevin Davies' header.
Having been booed off at half time, the Trotters started the second half much stronger with Guzan tipping Chris Eagles' strike around the post.
And the home side got themselves back into the game after 55 minutes when Klasnic was the first to react in the box after Villa failed to clear a corner.
Villa almost struck back immediately through Bent, but Cahill slid in to deflect his goalbound shot wide.
Then Mark Davies came close to a Wanderers' leveller but drilled his shot on the edge of the box past the post.
Goalscorer Klasnic went off injured late on as Coyle brought on David Ngog and Gael Kakuta in search of an equaliser.
But it was Villa who came closest to scoring again, as Jaaskelainen had to be alert to save from Albrighton in injury time.
Bolton: Jaaskelainen, Boyata, Cahill, Knight, Robinson, Sanli (Kakuta 71), Pratley, Mark Davies, Eagles, Kevin Davies, Klasnic (Ngog 78). Subs not used: Bogdan, Steinsson, Muamba, Petrov, O'Halloran. Booked: Mark Davies. Goals: Klasnic 55.
Aston Villa: Guzan, Hutton, Dunne, Collins, Warnock, Albrighton, Herd, Petrov, N'Zogbia, Bent (Heskey 81), Agbonlahor. Subs not used: Marshall, Ireland, Delfouneso, Clark, Bannan, Weimann. Booked: Albrighton, Agbonlahor. Goals: Albrighton 33, Petrov 39.