Cushing’s side wasted a host of chances during the game and a stalemate seemed a certainty until Houghton’s timely free-kick.
"I'm proud of the players as we didn't force it, we moved it around I thought we deserved the goal,” he said.
"We have a strategy when it comes to recruitment here and we got the players we wanted and we can also push up our development squad players or all that money would be wasted if we don't promote from within.
"We trust our squad and the 16 we have, with five also sitting in the stands as well as players who are injured, we have the players to replace them, it’s a tight squad and a small squad but a talented squad.
"We just want to play our game, work hard, create chances and try and win the game and we'll go into every game this season with the aim of winning.
"We always go to the end and we learnt from the Notts County game last year when we didn't go to the end but I think the team really pulled together and really wanted the goal and I think a draw would have felt like a loss."
The away side were first to find their feet and should have opened the scoring after Jess Clarke was bundled over in the box, only for the England winger to put the penalty wide.
City began to create chances as they stepped up the pressure with Kosovare Asllani firing a volley over the bar, whilst Magpies keeper Megan Walsh got a crucial hand to divert the ball away from a number of waiting players.
A trailing foot from Dani Buet on Nikita Parris allowed City the chance to take the lead from the spot, but Walsh superbly saved from Toni Duggan to keep the score’s level, before Asllani’s tap in was ruled offside, just moments later.
City continued to press with Buet clearing off the line for a second time, with Nick Cushing’s side unlucky to go into the break level.
The second-half began as the first ended, with the home side pushing for the opening goal but the Notts defence were in bullish mood, limiting the hosts to half chances.
Scott wasted another chance, firing over just outside the six-yard box as home fans frustrations began to surface.
Duggan's deflected shot went narrowly wide but it was Houghton's 30-yard free-kick with seconds remaining that got City the hard earned victory, with the ball bouncing over keeper Walsh.
Notts County manager Rick Passmoor said: "Being 30 seconds away from what we could call the masterplan, especially playing against a terrific team away from home.
“We've worked our socks off and played very, very well but we've given away an awful free-kick and it’s tough for her (Megan Walsh) as she's had a stormer of a game.
"It’s a great step in the right direction and I’m really pleased but I’m also disappointed because to come here and get a point, already would have dimmed their progress and obviously give us a lot of confidence.
"We're a small knit group and a small squad and let’s learn from it and we've got Arsenal next and I’m sure if we can keep putting out that eleven with that attitude, we'll be ok in the WSL.
"The WSL game is evolving into a possession based game and being technically and tactically comfortable in possession, so all pre-season we've done that and its looked really great.
"You can't come to Manchester City and just have that side of the game, so we've had one day's preparation on the pitch and in the classroom giving them different scenario's and we were 30 seconds away from absolutely nailing it.
“The players will be disappointed but they've got to be proud of what they've achieved tonight, because if they do that, we're going to win more this season that we lose."
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Manchester City (4-4-2): Karen Bardsley, Lucy Bronze, Demi Stokes, Steph Houghton, Abbie McManus, Daphne Corboz, Jill Scott, Kosovare Asllani, Toni Duggan, Jane Ross, Nikita Parris
Substitutes Not Used: Marie Hourihan, Zoe Tynan, Alethea Paul, Jennifer Beattie, Amelia Kemp
Bookings: McManus 72
Red Cards:
Notts County (4-4-2): Megan Walsh, Maja Krantz, Sophie Bradley-Auckland, Amy Turner, Dani Buet, Leanne Crichton, Angharad James, Rachel Yankey, Jess Clarke, Rachel Williams, Ellen White
Substitutes: Aileen Whelan on for White 83
Substitutes Not Used: Carly Telford, Aivi Luik, Alice Hassall, Laura-Jayne O’Neill
Bookings:
Red cards:
Attendance: 1,195
Referee: Joseph Johnson
